Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 69 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 19014 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 48 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 68 structure 24 protein 22 RNA 12 dna 11 sequence 11 figure 10 cell 9 SARS 9 NMR 9 Fig 8 study 8 peptide 8 model 7 result 7 University 6 residue 5 interaction 5 high 5 activity 5 acid 5 PDB 5 Institute 4 virus 4 method 4 membrane 4 bind 4 amino 4 Department 3 molecular 3 function 3 drug 3 domain 3 change 3 Lys 3 HPLC 3 Gly 3 Fmoc 3 ATP 2 synthesis 2 surface 2 site 2 secondary 2 region 2 receptor 2 process 2 molecule 2 lipid 2 fret 2 form 2 fluorescence Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 10479 protein 8651 structure 5417 peptide 4014 cell 2866 interaction 2865 sequence 2674 acid 2594 membrane 2448 study 2352 activity 2334 model 2220 method 2213 residue 2058 molecule 1874 result 1770 site 1741 domain 1681 function 1538 receptor 1536 analysis 1518 effect 1413 region 1379 system 1344 datum 1326 process 1320 group 1299 surface 1298 drug 1286 approach 1282 virus 1273 amino 1261 property 1255 mechanism 1254 ligand 1248 complex 1177 enzyme 1150 formation 1142 type 1142 role 1142 energy 1141 binding 1134 chain 1111 - 1095 lipid 1088 time 1075 compound 1065 % 1045 inhibitor 1038 target 1038 number Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1808 RNA 1397 al 1228 et 1215 . 691 C 671 NMR 656 University 508 Fig 466 SARS 403 II 382 PDB 361 N 327 Institute 311 S. 311 A 306 DNA 303 pH 300 M. 296 E. 294 Protein 259 MD 255 K 255 Department 251 D 248 MS 245 A. 242 de 230 CoV-2 224 HIV-1 222 P. 222 C. 217 J. 216 M 212 S 209 Molecular 201 B 199 Italy 198 L 196 Gly 195 fl 193 EM 191 T 186 Structure 183 Germany 181 SEM 179 L. 177 Chemistry 175 R. 173 CD 171 Ca Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 6021 we 2856 it 966 they 551 i 421 them 257 us 101 itself 95 one 33 themselves 25 you 18 he 6 me 3 she 2 u 2 s 2 ppifs 2 ourselves 2 glycomapsdb 2 cb562 1 ™ 1 ³hser 1 yegfp 1 upa 1 tlg1 1 theirs 1 sod-3::gfp 1 pcp4l1 1 p110a 1 ours 1 o*-orbital 1 n−3 1 mrnas 1 mine 1 iv-3l3r. 1 insl3 1 i-[(3'-allyl-2'-hydroxybenzilidene)amino]-3-hydroxyguanidine 1 https://researchdata.bath.ac.uk/772/ 1 his 1 himself 1 him 1 herg 1 glycoprotdb 1 flexpepdock 1 fbp17 1 eman2 1 cys1-cys6 1 asap2 1 6.5Å 1 's Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 38396 be 7267 have 5658 use 2895 show 2787 bind 2195 base 1431 find 1379 form 1258 contain 1144 study 1129 determine 1088 provide 1082 include 1033 obtain 999 know 981 suggest 976 identify 927 involve 923 develop 884 investigate 882 allow 876 increase 838 do 827 observe 789 induce 770 present 765 compare 760 reveal 757 predict 739 perform 733 lead 724 make 671 follow 666 report 662 result 654 give 642 require 629 indicate 628 describe 616 synthesize 605 associate 599 apply 594 design 589 generate 582 characterize 575 demonstrate 554 produce 550 represent 533 relate 527 fold Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 2406 not 2186 also 2136 high 2106 structural 2105 - 2039 different 1892 molecular 1716 such 1533 more 1532 other 1463 well 1455 new 1302 human 1128 however 1123 large 1114 small 1076 specific 1073 most 1062 biological 1037 only 1010 important 1004 several 1003 secondary 996 active 993 single 974 low 874 functional 853 as 844 many 818 first 811 conformational 777 non 761 thus 730 very 682 various 680 possible 679 novel 671 similar 663 highly 625 experimental 619 here 612 free 593 therefore 588 long 583 then 566 further 562 like 556 potential 555 same 547 viral Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 331 most 184 good 129 least 89 high 82 Most 52 large 44 low 26 small 25 strong 25 near 23 short 22 simple 21 late 20 great 17 close 13 long 9 fast 7 early 5 slow 4 big 4 bad 4 -peptides 3 weak 3 new 2 tight 2 thick 2 outermost 2 old 2 easy 2 deep 2 -which 2 -methylated 2 -hybrid 1 ψ 1 ~250nt 1 wide 1 steep 1 soft 1 slim 1 rugosa 1 quick 1 preS1 1 poor 1 pdqu 1 micrometre 1 linkedgalactose 1 leftmost 1 i+1 1 firm 1 fine Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 742 most 92 least 32 well 2 smallest 2 shortest 2 highest 1 worst 1 fast 1 -spectroscopic Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 10 www.rcsb.org 7 www 3 www.wwpdb.org 3 www.molinspiration.com 3 www.drugbank.ca 3 tox.charite.de 3 proteinmodel.org 3 glycam.org 2 zinc.docking.org 2 www.openrasmol.org 2 www.glycanstructure.org 2 www.eyesopen.com 2 www.dovepress.com 2 www.chembridge.com 2 researchdata.bath.ac.uk 2 pubchem.ncbi.nlm.nih.gov 2 glytoucan.org 2 gitlab.com 2 en.wikipedia.org 2 doi.org 2 dev.glycam.org 2 cdn.rcsb.org 2 abcis.cbs.cnrs.fr 1 www.uniprot.org 1 www.unicarbkb.org 1 www.swisstargetprediction.ch 1 www.rna.it-chiba.ac.jp 1 www.organ.su.se 1 www.nobelprize.org 1 www.ncbi 1 www.mgc.ac.cn 1 www.mdli.com 1 www.litemol.org 1 www.knme.org 1 www.ionis 1 www.hyper.com 1 www.glycosciences.de 1 www.fbs.osaka-u.ac.jp 1 www.eyesopen 1 www.expasy.org 1 www.elsevier.com 1 www.eidogen.com 1 www.drugbank 1 www.cengent.com 1 www.biochem.ucl.ac.uk 1 www.bindingdb.org 1 www.bayerhealthcare.com 1 www.accelrys.com 1 www-cryst.bioc.cam.ac.uk 1 webofknowledge.com Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 7 http://www 3 http://www.rcsb.org 2 http://zinc.docking.org 2 http://www.wwpdb.org/documentation/carbohydrate-remediation 2 http://www.rcsb.org/pdb 2 http://www.rcsb.org/ 2 http://www.openrasmol.org/ 2 http://www.molinspiration.com/ 2 http://www.glycanstructure.org/ 2 http://www.chembridge.com 2 http://tox.charite.de/protox_II 2 http://researchdata.bath.ac.uk/772/ 2 http://pubchem.ncbi.nlm.nih.gov/ 2 http://proteinmodel.org/AS2TS/STRALSV/ 2 http://glytoucan.org/ 2 http://gitlab.com/glyconavi/pdb2glycan 2 http://dev.glycam.org/portal/gf_home/ 1 http://www.wwpdb.org/ 1 http://www.uniprot.org/ 1 http://www.unicarbkb.org/) 1 http://www.swisstargetprediction.ch 1 http://www.rna.it-chiba.ac.jp/ 1 http://www.rcsb.org/structure/6M2N 1 http://www.rcsb.org/stats/growth/growth-released-structures 1 http://www.rcsb.org/pdb/ 1 http://www.organ.su.se/gw/doku.php?id=3dcfg 1 http://www.nobelprize.org/prizes/chemistry/2017 1 http://www.ncbi 1 http://www.molinspiration.com 1 http://www.mgc.ac.cn/DBatVir/ 1 http://www.mdli.com 1 http://www.litemol.org/ 1 http://www.knme.org 1 http://www.ionis 1 http://www.hyper.com/?tabid=360 1 http://www.glycosciences.de/database/start.php?action=form_pdb_data 1 http://www.fbs.osaka-u.ac.jp/labs/yanagida/ 1 http://www.eyesopen.com/rocs 1 http://www.eyesopen.com 1 http://www.eyesopen 1 http://www.expasy.org/ 1 http://www.elsevier.com/advanced-search 1 http://www.eidogen.com 1 http://www.drugbank.ca/drugs/DB00041 1 http://www.drugbank.ca/drugs/DB00007 1 http://www.drugbank.ca/ 1 http://www.drugbank 1 http://www.dovepress.com/testimonials.php 1 http://www.dovepress.com/drug-design-development-and-therapy-journal 1 http://www.cengent.com Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 thalmann@ics-cnrs.unistra.fr 1 stamou@nano.ku.dk 1 s.sharkh@hzdr.de 1 roumestand@cbs.cnrs.fr 1 pilar.riveragil@physik.uni-marburg.deth 1 ohki@bio.phys.tohoku.ac.jp 1 nax3@cdc.gov 1 michael.graetzel@epfl.ch 1 markus.staufenbiel@biologie.unio 1 krishna.bhattiprolu@uni-graz.at 1 kissel@staff.uni-marburg.de 1 jrother@gwdg.de 1 janaspe@csse.uwa.edu.au 1 gpaehle@gwdg.de 1 g.helms@jacobs-university.dein 1 ehrlich@nano.ku.dk 1 cweichb@gwdg.de 1 christian.schwieger@chemie.uni-halle.de 1 anna.pietuch@chemie.unigoettingen.de 1 amit@ccmb.res.in 1 a.m.van.oijen@rug.nl 1 thomas.andresen@nanotech.dtu.dk 1 mihaela.mic@itim-cj.ro 1 mara.kozic@liverpool.ac.uk Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 10 protein is not 9 data are available 7 protein binding sites 6 proteins are often 6 receptor binding site 6 structure is not 6 structures are also 5 domains do not 5 peptides are able 5 peptides are more 5 peptides were also 5 structures are available 5 structures including pseudoknots 4 activity is not 4 activity was also 4 function is still 4 interactions are important 4 interactions are not 4 membranes is essential 4 methods are more 4 model is able 4 molecules are not 4 peptide was able 4 peptides are also 4 proteins are very 4 proteins do not 4 proteins is not 4 receptor binding domain 4 results provide new 4 sequence is not 4 structure does not 4 structure is also 4 structures are not 4 structures have also 4 structures is important 3 activity is also 3 activity is still 3 activity was not 3 cell is highly 3 data are often 3 data presented here 3 data were not 3 effect has not 3 effects are not 3 groups has consistently 3 method has also 3 method is highly 3 model was also 3 peptide binding sites 3 peptide does not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 process are not fully 2 rna have not yet 1 acid is not very 1 acids are not equally 1 acids are not visible 1 activity is not always 1 activity is not exclusive 1 activity was not due 1 analysis is not possible 1 cells are not able 1 cells are not well 1 data are not available 1 data revealed no significance 1 data were not available 1 data were not suitable 1 domain has no significant 1 domain is not yet 1 domains are not well 1 domains do not appreciably 1 domains do not easily 1 effect has not yet 1 effect was not significant 1 effects are not completely 1 effects are not simple 1 function are not still 1 function is not completely 1 functions were not significantly 1 groups revealed no statistically 1 interactions are not due 1 interactions are not sufficient 1 interactions are not symmetrical 1 interactions are not well 1 interactions is not translatable 1 membranes are not easy 1 membranes are not visible 1 method is not exhaustive 1 method is not generally 1 methods are not suffi 1 methods are not sufficiently 1 molecule does not completely 1 molecules are not real 1 molecules are not specific 1 molecules is not haemolytic 1 peptide is not effi 1 peptide showed no hemolytic 1 peptides are not ideal 1 peptides are not stable 1 peptides do no exhibit 1 peptides have no structure 1 peptides show no pressor A rudimentary bibliography -------------------------- id = cord-018133-2otxft31 author = Altman, Russ B. title = Bioinformatics date = 2006 keywords = datum; dna; information; sequence; structure summary = Experimentation and bioinformatics have divided the research into several areas, and the largest are: (1) genome and protein sequence analysis, (2) macromolecular structure-function analysis, (3) gene expression analysis, and (4) proteomics. With the completion of the human genome and the abundance of sequence, structural, and gene expression data, a new field of systems biology that tries to understand how proteins and genes interact at a cellular level is emerging. The Entrez system from the National Center for Biological Information (NCBI) gives integrated access to the biomedical literature, protein, and nucleic acid sequences, macromolecular and small molecular structures, and genome project links (including both the Human Genome Project and sequencing projects that are attempting to determine the genome sequences for organisms that are either human pathogens or important experimental model organisms) in a manner that takes advantages of either explicit or computed links between these data resources. doi = 10.1007/0-387-36278-9_22 id = cord-010260-8lnpujip author = Anthonsen, Henrik W. title = The blind watchmaker and rational protein engineering date = 1994-08-31 keywords = Fig; NMR; electrostatic; method; protein; sequence; structure summary = In the present review some scientific areas of key importance for protein engineering are discussed, such as problems involved in deducting protein sequence from DNA sequence (due to posttranscriptional editing, splicing and posttranslational modifications), modelling of protein structures by homology, NMR of large proteins (including probing the molecular surface with relaxation agents), simulation of protein structures by molecular dynamics and simulation of electrostatic effects in proteins (including pH-dependent effects). In the present review we will look at the design part of the protein engineering process, with emphasis on some of the more difficult steps, especially homology based modelling in cases with very low sequence similarity, nuclear magnetic resonance (NMR) of very large proteins and modelling of electrostatic interactions. They modify properties of individual residues and of the protein, and may thus make surface prediction, dynamics simulations and structural modelling in general more complex. doi = 10.1016/0168-1656(94)90152-x id = cord-015642-p46abodr author = Backofen, Rolf title = Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures date = 2013 keywords = RNA; structure summary = On a more technical level, the problem to compute the partition function over RNA secondary structures with given end-to-end distance d, usually measured as the number of external bases (plus possibly the number of structural domains) arises for instance when predicting nucleic acid secondary structure in the presence of single-stranded binding proteins [9] or in models of RNA subjected to pulling forces (e.g. in atom force microscopy or export through a small pore) [10, 23, 11] . can be split as follows, This gives the recursion [10] , the investigate of loop entropy dependence [7] , the analysis of FRET signals in the presence of single-stranded binding proteins [9] , as well as in mathematical studies of RNA panhandle-like structures [2, 13] . As the graph-distance for a pair of nucleotides in a given secondary structure can be computed in O(n log n) time, even large samples can be evaluated efficiently 2 . The equilibrium partition function and base pair binding probabilities for RNA secondary structure doi = 10.1007/978-3-642-40453-5_10 id = cord-330427-3eoio8uk author = Bassetto, Marcella title = Structural biology in antiviral drug discovery date = 2016-09-06 keywords = figure; inhibitor; structure summary = doi = 10.1016/j.coph.2016.08.014 id = cord-257494-242k58ll author = Bastos, Paulo title = Human Antimicrobial Peptides in Bodily Fluids: Current Knowledge and Therapeutic Perspectives in the Postantibiotic Era date = 2017-01-17 keywords = LL-37; activity; amp; antimicrobial; cell; gram; human; peptide; structure summary = 1 Human host defense peptides are an intrinsic part of the innate immune system and exhibit a broad activity spectrum against bacteria, fungi, viruses, and parasites While AMPs can be antibacterial (ABPs), antifungal, antiprotist, antiviral, anticancer, antiparasitic, insecticidal, spermicidal, chemotactic, antioxidant, protease inhibitors, or even exhibit wound healing properties (Supporting Information Table S1), their scope of action overlaps considerably and some peptides show activity at several levels (Fig. 2 ). 75 Moreover, when stabilizing disulfide bridges between conserved cysteine residues in human AMPs with β-hairpin or β-sheet conformations are disrupted, the resulting linear peptides still maintain their antimicrobial properties despite losing membranolytic activity. 212, 213 However, it should be noted that the antimicrobial effects of encephalins and their derived peptides result mostly from animal studies and have not been adequately studied in human secretions, despite the high conservation of their sequences across species, which most likely contribute for the similar activity spectrum. doi = 10.1002/med.21435 id = cord-002490-kw8psrmz author = Beniac, Daniel R. title = Structure of the Ebola virus glycoprotein spike within the virion envelope at 11 Å resolution date = 2017-04-11 keywords = Ebola; Fig; structure summary = We present the structure of the surface Ebola virus (EBOV) trimeric glycoprotein (GP) spike at 11 Å resolution, in situ within the viral plasma membrane of purified virus particles. In addition, 29,976 images were selected for reference-free analysis of the half-diameter of EBOV to investigate the spatial distribution of the GP spikes, as well as the periodicity and symmetrical relationships between GP and the matrix protein VP40 in the envelope, and the underlying nucleocapsid layer (Figs 1c and S3) . The spike structure of Beniac et al imaged within the virus-like particles was somehow clipped, since this should have included the mucin-like domains: in addition, tomography was combined with single-particle analysis, which may have distorted the results 4 . The structure that we report here is based entirely on the well-accepted method of single-particle analysis using projection matching, and is broadly similar to that published of expressed GP in virus-like particles using tomography 28, 29 : there are noticeable differences in shape and size of the spike, as well as in resolution (Fig. 4) . doi = 10.1038/srep46374 id = cord-278135-kvuti410 author = Benjin, Xu title = Developments, applications, and prospects of cryo‐electron microscopy date = 2019-12-26 keywords = cryo; structure summary = Blue corresponds to structures determined by X-ray crystallography, dark orange corresponds to structures determined by nuclear magnetic resonance, and gray corresponds to structures determined by electron microscopy and NMR, cryo-EM has the following advantages: (a) it does not need crystals; (b) it is suitable for proteins and their complexes of large molecular weight; (c) it reduces radiation damage and maintains the native activity and functional state of samples, including posttranslational modifications; (d) multiple different conformational states can be captured in one experiment; (e) it is suitable for the structural analysis of membrane proteins such as GPCR and their complexes; (f) when encountering some structures that cannot be resolved by conventional X-ray crystallography, cryo-EM is still the mainstream. doi = 10.1002/pro.3805 id = cord-283491-y6t64pux author = Brzezinski, Dariusz title = Covid‐19.bioreproducibility.org: A web resource for SARS‐CoV‐2‐related structural models date = 2020-09-27 keywords = PDB; SARS; structure summary = Understandably, firstline research findings, including molecular structure determinations, depositions in the Protein Data Bank (PDB), 1 and related results, are often made public on BioRxiv 2 or MedRxiv 3 before formal peer review. In this paper, we present covid-19.bioreproduciblity.org, a web resource that organizes SARS-CoV-2 related structural information in a way that should be understandable and useful for a wider scientific community, and not only for structural biologists. Finally, the structures are evaluated by a team of expert structural biologists who use a combination of the mined data, validation reports, and manual inspection of the protein models and associated electron density to examine potential problems. If raw diffraction data are available, the results of automatic processing of images by HKL-3000auto are examined to verify that the structure was determined in the correct space group and at optimal resolution. doi = 10.1002/pro.3959 id = cord-171099-d0qr84xg author = Buehler, Markus J. title = Nanomechanical sonification of the 2019-nCoV coronavirus spike protein through a materiomusical approach date = 2020-03-30 keywords = protein; sound; structure; virus summary = Presenting musical encoding in two versions one in the amino-acid scale and one based on equal temperament tuning the method allows for expressing protein structures in audible space, offering novel avenues to represent, analyze and design architectural features across lengthand time-scales. We further report a hierarchical frequency spectrum analysis of five distinct protein structures, which offer insights into how genetic mutations, and the binding of the virus spike protein to the human ACE2 cell receptor directly influence the audio. What you hear is a multi-layered algorithmic composition featuring both the vibrational spectrum of the entire protein (expressed in sound and rhythmic elements), the sequence and folding of amino acids that compose the virus spike structure, as well as interwoven melodiesforming counterpoint music -reflecting the complex hierarchical intersecting geometry of the protein. doi = nan id = cord-002015-s3tdllby author = Burton, Aaron S. title = The elusive quest for RNA knots date = 2016-02-01 keywords = RNA; knot; structure summary = 2, 3 It is therefore a remarkable fact that the statistical incidence of topological entanglement in biomolecules such as proteins and DNA filaments, which are both long and compact, is substantially smaller than expected for general models of equilibrated polymers with equivalent length and packing conditions. It is accordingly plausible, as remarked by Levinthal in more general contexts, 7,8 that protein sequences have evolved to encode not only the thermodynamically-stable native fold, but also the sequence of steps leading to the native structure formation so to minimize the incidence of misfolded states, including knotted ones which would be very challenging to backtrack. It is possible that the sequence of naturally-occurring RNAs, some of which need to be efficiently translocated through biological pores, have evolved to harness folding kinetics and thermodynamics so as to minimize the incidence of various forms of selfentanglement, including knots, in their native structures. doi = 10.1080/15476286.2015.1132069 id = cord-008588-4eu9v5d3 author = Chastain, Michael title = Structural Elements in RNA date = 2008-02-29 keywords = NMR; RNA; dna; structure summary = The structures of the tRNA anticodon loop and the UUCG loop suggest that the specific loop sequences adopt conformations that are more stable because they contain more hydrogen bonding and stacking interactions-particularly interactions with the sugar-phosphate backbone. Determining the conformation of these loops in RNA is important for understanding how these nucleotides interact with other elements of secondary structure to form tertiary interactions and for understanding how proteins bind to bulge loops. In general, this could occur between any of the secondary structure regions containing unpaired nucleotides (single-stranded regions, hairpin loops, bulge loops, internal loops, and junction loops). There are several examples of RNA molecules containing tertiary contacts between nucleotides that are in loop regions of secondary structure. The high frequency with which known RNA structures contain tertiary pairing between nucleotides that are unpaired in the secondary structure stresses the importance of learning more about such interactions. doi = 10.1016/s0079-6603(08)60008-2 id = cord-314321-klb8oe9q author = Chen, Serena H. title = Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets date = 2020-04-18 keywords = SARS; protein; structure summary = doi = 10.1101/2020.04.17.047548 id = cord-329504-91te3nu8 author = Croll, Tristan title = Making the invisible enemy visible date = 2020-10-07 keywords = PDB; RNA; SARS; structure summary = A general indication of how well the atomic model fits the measurement data can be obtained by comparing the deposited R-factors to results from PDB-REDO (10) (including Whatcheck (11)) to determine the overall density fit as well as many other diagnostics. Our remodelled structure is offering a valuable structural basis for future studies, such as in-silico docking and drug design targeting at SARS-CoV-2 RdRp (34), as well as for computational modelling or simulations to investigate the molecular mechanism of viral replication (31, 35, 36) . This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities. doi = 10.1101/2020.10.07.307546 id = cord-346546-yffwd0dc author = Douangamath, Alice title = Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease date = 2020-05-27 keywords = SARS; figure; fragment; structure summary = To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease. For 113 another series of hit compounds, containing a N-chloroacetyl piperidinyl-4-carboxamide 114 motif (Table S2 ) which displays lower reactivity and were not frequent hitters in previous 115 screens, we attempted crystallization despite their absence of labelling in the stringent 116 The bound fragments comprehensively sample all subsites of the active 287 site revealing diverse expansion vectors, and the electrophiles provide extensive, systematic 288 as well as serendipitous, data for designing covalent compounds. Crystal structure of SARS-CoV-2 main protease 763 provides a basis for design of improved alpha-ketoamide inhibitors doi = 10.1101/2020.05.27.118117 id = cord-282035-jibmg4ch author = Dunbar, R. I. M. title = Structure and function in human and primate social networks: implications for diffusion, network stability and health date = 2020-08-26 keywords = Dunbar; individual; layer; network; size; social; structure summary = doi = 10.1098/rspa.2020.0446 id = cord-322885-ob5euspo author = Durdagi, Serdar title = Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing date = 2020-09-09 keywords = 7CWB; 7cwc; Fig; Mpro; SARS; drug; structure summary = One Sentence Summary Radiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19. Radiation-damage-free SFX method which enables obtaining the novel high-resolution ambient-temperature structures of the binding pocket of Mpro provides an unprecedented opportunity for identification of highly effective inhibitors for drug repurposing by using a hybrid approach that combines structural and in silico methods. We determined two radiation-damage-free SFX crystal structures of SARS-CoV-2 Mpro in two crystal forms at 1.9 Å and 2.1 Å resolutions with the following PDB IDs: 7CWB and 7CWC, respectively (Fig. 1A, B) (Supplementary Table 1&2 The diffraction data collected remotely at the MFX instrument of the LCLS at SLAC National Laboratory, Menlo Park, CA (Sierra et al., They reveal novel active site residue conformations and dynamics at atomic level, revealing several differences compared to the prior ambient-temperature structure of SARS-CoV-2 Mpro that was obtained at a home X-ray source (Fig. 1A, B ). doi = 10.1101/2020.09.09.287987 id = cord-033010-o5kiadfm author = Durojaye, Olanrewaju Ayodeji title = Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study date = 2020-10-02 keywords = Fig; SARS; model; protein; sequence; structure summary = RESULTS: This study describes the detailed computational process by which the 2019-nCoV main proteinase coding sequence was mapped out from the viral full genome, translated and the resultant amino acid sequence used in modeling the protein 3D structure. Our current study took advantage of the availability of the SARS CoV main proteinase amino acid sequence to map out the nucleotide coding region for the same protein in the 2019-nCoV. The predicted secondary structure composition shows a high degree of alpha helix and beta sheets, respectively, occupying 45 and 47% of the total residues with the percentage loop occupancy at 8% regarded as comparative modeling, constructs atomic models based on known structures or structures that have been determined experimentally and likewise share more than 40% sequence homology. doi = 10.1186/s43042-020-00081-5 id = cord-102463-d440jsek author = Eguchi, Raphael R. title = IG-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation date = 2020-08-10 keywords = VAE; figure; structure summary = doi = 10.1101/2020.08.07.242347 id = cord-252166-qah877pk author = Ekins, S title = In silico pharmacology for drug discovery: applications to targets and beyond date = 2007-09-01 keywords = Ekins; QSAR; drug; model; molecule; structure summary = These in silico methods include databases, quantitative structure-activity relationships, similarity searching, pharmacophores, homology models and other molecular modeling, machine learning, data mining, network analysis tools and data analysis tools that use a computer. This included the development of methods and databases, quantitative structure-activity relationships (QSARs), similarity searching, pharmacophores, homology models and other molecular modelling, machine learning, data mining, network analysis and data analysis tools that all use a computer. For example, one study used probabilistic neural networks with 24 atom-type descriptors to classify 799 molecules from the MDL Drug Data Reports (MDDR) database with activity against one of the seven targets (G protein-coupled receptors (GPCRs), kinases, enzymes, nuclear hormone receptors and zinc peptidases) with excellent training, testing and prediction statistics (Niwa, 2004) . In silico pharmacology for drug discovery S Ekins et al derived with 40 molecules with activities over three log orders to result in a five-feature pharmacophore model. doi = 10.1038/sj.bjp.0707306 id = cord-355327-d3gcfepx author = Fan, Samuel W title = Conformational changes in redox pairs of protein structures date = 2009-08-01 keywords = Cys; Redox; change; disulfide; protein; structure summary = Several classes of structural changes were observed, proteins that exhibit: disulfide oxidation following expulsion of metals such as zinc; major reorganisation of the polypeptide backbone in association with disulfide redox-activity; order/disorder transitions; and changes in quaternary structure. These groups were: proteins that oxidize disulfides following expulsion of metals such as Zn; proteins that exhibited major reorganization or ''''morphing'''' of portions of the polypeptide backbone in association with disulfide redox-activity; proteins that exhibited order/disorder transitions; and proteins that exhibited changes in quaternary structure. Twenty-nine Redox Pair protein clusters with intermolecular disulfide bonds exhibit changes in quaternary structure upon oxidation/reduction. We were previously aware of two instances where subdomain morphing of proteins has been associated with reversible disulfide reduction: a redox-controlled structural reorganization of the ion channel CLIC1 proposed to regulate its insertion into membranes, 18 and sequential oxidation of the transcription factor OxyR in response to oxidative stress which modulates its quaternary structure and DNA-binding properties. doi = 10.1002/pro.175 id = cord-003020-q69f57el author = Farhadi, Tayebeh title = Computer-aided design of amino acid-based therapeutics: a review date = 2018-05-14 keywords = acid; amino; design; peptide; protein; structure summary = Computational techniques play a key role to design and develop the amino acid-based therapeutics such as proteins, peptides and peptidomimetics. Here, the elaborated techniques that are developed to characterize the amino acid sequences consistent with a specific structure and allow protein design are discussed. 3 Recently, pharmaceutical scientists have shown interest in engineering amino acid-based therapeutics such as proteins, peptides and peptidomimetics. Computer-aided design of amino acid-based therapeutics Fixing the backbone decreases the computational complication, but it may inhibit the main chain modifications to adjust sequence alternation. Computer-aided design of amino acid-based therapeutics to model peptide binding to targets of interest. 28, 134 Sequence-based method Recently, a method has been developed to rank peptide compound matches that are limited to short linear motifs in proteins and compounds with amino acid substituents. doi = 10.2147/dddt.s159767 id = cord-007373-livz5zuu author = Gayathri, P. title = Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket date = 2006-03-15 keywords = Fig; domain; protease; residue; structure summary = authors: Gayathri, P.; Satheshkumar, P.S.; Prasad, K.; Nair, Smita; Savithri, H.S.; Murthy, M.R.N. title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket In the present study, the crystal structure of SeMV protease domain was determined to a resolution of 2.4 Å by multiple isomorphous replacement coupled with anomalous scattering, with a view to identify the residues involved in substrate binding as well as protease -VPg interactions. The absence of well-defined density for F301 in SeMV protease suggests that its side chain might undergo substantial displacement on binding of the substrate or on conformational changes induced by the interaction of the protease domain with VPg. TEV and equine arteritis virus proteases, in which a serine residue occurs at the position corresponding to F301, are active in trans. doi = 10.1016/j.virol.2005.11.011 id = cord-009660-23cdi61w author = Györkey, Ferenc title = Electron microscopic observations on structures resembling myxovirus in human sarcomas date = 2006-06-27 keywords = structure summary = Herpes, adeno-and reoviruses, as well as elementary bodies of mycoplasma, occasionally occur in human tumors probably as passengers and not -~ as etiologically important agents.1~8~20 Occasionally, type C and related virus-like particles were found in neoplastic tissues deriving from human leukemia, lymphoma, and sarcoma.8J6 T h e number of these particles rapidly diminishes in cells cultured in vitro; thus, these viruslike particles have never been identified as the human counterparts of oncogenic type C viruses of animals. Preliminary findings concerning such structures, however, have recently been reported by Stewart36 who observed the occurrence of filamentous structures and budding type Clike virus particles in tissue cultures of human liposarcoma and Hodgkin''s disease. T h e present paper is a preliminary report on morphological observations concerning structures that may be of viral derivation, as found in biopsies and tissue cultures of human tumors of mesenchymal origin. doi = 10.1002/1097-0142(197106)27:6<1449::aid-cncr2820270627>3.0.co;2-3 id = cord-354465-5nqrrnqr author = Haslinger, Christian title = RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties date = 1999 keywords = RNA; graph; secondary; sequence; structure summary = Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture. Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture. In case of one particular class of biopolymers, the ribonucleic acid (RNA) molecules, decoding of information stored in the sequence can be properly decomposed into two steps: (i) formation of the secondary structure, that is, of the pattern of Watson-Crick (and GU) base pairs, and (ii) the embedding of the contact structure in three-dimensional space. On the other hand, an increasing number of experimental findings, as well as results from comparative sequence analysis, suggest that pseudo-knots are important structural elements in many RNA molecules (Westhof and Jaeger, 1992) . doi = 10.1006/bulm.1998.0085 id = cord-254107-02bik024 author = Hillisch, Alexander title = Utility of homology models in the drug discovery process date = 2004-08-31 keywords = homology; model; protein; structure summary = doi = 10.1016/s1359-6446(04)03196-4 id = cord-325328-3l3jznkj author = Holbrook, Stephen R title = RNA structure: the long and the short of it date = 2005-05-16 keywords = RNA; motif; structure summary = Structural studies and comparative sequence analyses have suggested that biological RNAs are largely modular in nature, composed primarily of conserved structural building blocks or motifs [4] of secondary (helices, and internal, external and junction loops) and tertiary (coaxial stacks, kissing hairpin loops, ribose zippers, etc.) structure. Other structures include the specificity domains of both A[17] and B-type ribonuclease P [18 ] ; RNAs corresponding to a guanine-responsive riboswitch (xpt) complexed with guanine [19 ] or hypoxanthine [20] , and an adenosine-responsive riboswitch (add) complexed with adenosine [19 ] ; a highly conserved stem-loop motif found at the 3 0 end of the genome of SARS (severe acute respiratory syndrome) virus and other coronaviruses [21 ] ; the core encapsidation signal of MMLV [2 ] ; and complexes between a high-affinity RNA aptamer and the NF-kB p50 homodimer [22] , and between the archaeal RNAbinding protein L7Ae and an RNA K-turn derived from a H/ACA small RNA [23] . doi = 10.1016/j.sbi.2005.04.005 id = cord-266543-ng9zr299 author = Klebe, Gerhard title = Virtual ligand screening: strategies, perspectives and limitations date = 2006-06-20 keywords = HTS; docking; ligand; protein; structure summary = doi = 10.1016/j.drudis.2006.05.012 id = cord-018401-josb16pi author = Kumaraswamy, Priyadharshini title = Hierarchical Self-Assembled Peptide Nano-ensembles date = 2014-03-01 keywords = assembly; form; peptide; self; structure summary = Since peptide self-assembly is a bottom-up process where amino acids form the building blocks, it is easy to introduce functionalities on the carboxyl or amine terminal groups, opening up the possibilities of a wide range of chemical interactions leading to specific functions. These cyclic peptides have alternating D-and L-amino acids, which interact through intermolecular hydrogen bonding to form an array of self-assembled nanotubes with an internal diameter of 7-8 Å (Fig. 8.5 ). Peptide amphiphiles comprise of a hydrophilic head and hydrophobic tail that self-assemble in aqueous solution to form well-defined nanostructures like peptide bilayers, micelles, nanotubes, nanorods, and nanovesicles [64] [65] [66] . The topography of the self-assembled structures formed by two amphiphilic peptidolipids derived from the 31-35 residues of the amyloid beta peptide (C 18 -IIGLM-OH and C 18 -IIGLM-NH 2 ) was observed using this technique [99] . doi = 10.1007/978-3-642-31107-9_23 id = cord-329102-2y49kcwu author = Lan, Tammy C. T. title = Structure of the full SARS-CoV-2 RNA genome in infected cells date = 2020-06-30 keywords = FSE; RNA; SARS; figure; structure summary = We evaluated the robustness of our in-cell data derived genome-wide model by varying two critical RNA folding parameters used by RNAstructure: 1) the maximum allowed distance for base pairing and 2) the threshold for DMS signal normalization. Previous studies that computationally predicted genome-wide SARS-Cov-2 RNA structures used 1) RNAz, a thermodynamic-based model that additionally takes sequence alignment and considers base pairing conservation (Gruber et al., 2010; Rangan, Zheludev and Das, 2020) , and 2) Contrafold, which predicts RNA secondary structures without physics-based models and instead uses learned parameters based on known structures (Do, Woods and Batzoglou, 2006) . Interestingly, in silico predictions of the RNA structure of the SARS-CoV-2 genome using RNAz (Rangan, Zheludev and Das, 2020) and ScanFold (Andrews et al., 2020) do not find the 3-stem pseudoknot but instead support our in-cell model of Alternative Stem 1. doi = 10.1101/2020.06.29.178343 id = cord-013387-q91052qw author = Leão, Rozires P. title = Identification of New Rofecoxib-Based Cyclooxygenase-2 Inhibitors: A Bioinformatics Approach date = 2020-08-26 keywords = COX-2; LMQC50; LMQC72; compound; figure; lmqc36; structure summary = In this initial stage, the pivot molecule rofecoxib was used as a research model for the virtual screening in six commercial molecule databases: Chembridge DIVERSetEXP, DIVERSet CORE Library (https://www.chembridge.com) [24] , Maybridge Collections (www.maybridge.com) [25, 26] , ZINC Drug Database, ZINC Natural Stock (http://zinc.docking.org) [27] , and Drug FDA BindingDB (http://www.bindingdb.org) [27] using the programs Rapid Overlay of Chemical Structures (ROCS) and electrostatic similarity (EON). The bioactivity scores of the LMQC72, LMQC36, and LMQC50 structures were calculated for different parameters, as receptor binding of the ligand to the G protein coupled (GPCR) and nuclear receptor ligand, modulating ion channel, kinase inhibition, protease inhibition, and inhibition of enzyme activity. The bioactivity scores of the LMQC72, LMQC36, and LMQC50 structures were calculated for different parameters, as receptor binding of the ligand to the G protein coupled (GPCR) and nuclear receptor ligand, modulating ion channel, kinase inhibition, protease inhibition, and inhibition of enzyme activity. doi = 10.3390/ph13090209 id = cord-346965-0oq2n0af author = Liu, Zhi-Ping title = Bridging protein local structures and protein functions date = 2008-04-18 keywords = dna; function; local; method; protein; site; structure summary = The characteristics between interface and noninterface portions of a protein surface, such as sequence conservation, proportions of amino acids, secondary structure, solvent accessibility and side-chain conformational entropy, are often used to distinguish the specificity of local structures relating to protein binding function. The method relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologs. (2006) improved previous approaches by combining two known measures of ''functionality'' in proteins, i.e. cleft volume and residue conservation, to develop a method for identifying the location of ligand-binding pockets in proteins. (2006) applied an SVM method to predict DNA-binding sites using the features including amino acid sequence, profile of evolutionary conservation of sequence positions, and low-resolution structural information. (2006) developed a method to predict both protein-protein binding site location and interface type (obligate or non-obligate) using a Bayesian network in combination with surface patch analysis. doi = 10.1007/s00726-008-0088-8 id = cord-017181-ywz6w2po author = Maus, Carsten title = Component-Based Modelling of RNA Structure Folding date = 2008 keywords = RNA; base; model; structure summary = As this regulating process depends largely on structure formation, modelling of RNA folding would be a big step in the right direction for reflecting attenuation dynamics. Additionally, modelling interactions between mRNA and RNAP as well as mRNA and the ribosome are needed because both influence the kinetic folding process and RNA termination structures break up gene transcription. If observed structures are present during folding simulation, the macro level model can signalise this information and thus trigger dynamics to other components by adding new ports to itself (representing docking sites) or send messages over existing ports. Simulating the RNA folding with Kinfold [12] results in a five times higher amount of the 2-helix conformation than the single hairpin, but their total sum is about 60% of all molecules and thus less misfolded structures can be observed. The pattern observation function of the RNA folding model, which is realised at macro level, allows us to look for an intrinsic transcription termination structure [2] during simulation. doi = 10.1007/978-3-540-88562-7_8 id = cord-304794-z2kx314h author = Métifiot, Mathieu title = G-quadruplexes in viruses: function and potential therapeutic applications date = 2014-11-10 keywords = HIV-1; RNA; dna; figure; structure summary = Conversely, a G-quadruplex or G4 is formed by nucleic acid sequences (DNA or RNA) containing G-tracts or Gblocks (adjacent runs of guanines) and composed of various numbers of guanines. Short RNA templates from the central region of the HIV-1 genome contain G-rich sequences near the central polypurine tract (cPPT) at the 3 end of the pol gene (IN coding sequence); this is a region where one of the two primers used for synthesizing the (−) strand DNA is produced during reverse transcription. In addition, one could imagine alternative therapeutic strategies focused on targeting RNA structures within viral ORFs to interfere with the virus cycle as well as to promote antigen presentation and to stimulate the host immune response. Topology of a DNA G-quadruplex structure formed in the HIV-1 promoter: a potential target for anti-HIV drug development U3 Region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence doi = 10.1093/nar/gku999 id = cord-330590-nu8ckeud author = Nieto-Rabiela, F. title = Viral metacommunities associated to bats and rodents at different spatial scales date = 2018-12-30 keywords = clementsian; host; structure summary = doi = 10.1556/168.2018.19.2.9 id = cord-351222-9bfchw4u author = Rollinger, Judith M. title = Virtual screening for the discovery of bioactive natural products date = 2008 keywords = drug; natural; screening; structure; virtual summary = Some examples using high throughput docking as a structure-based virtual screening tool will be given here: Liu and Zhou applied a theoretical approach to find natural ligands as potential inhibitors of the SARS-CoV protease, a virus target of the severe acute respiratory syndrome [35] . Barreca and co-authors developed a 3D structure-based pharmacophore model with LIGANDSCOUT for the discovery of new scaffolds acting as HIV-1 non-nucleoside reverse transcriptase inhibitors by virtual screening of large chemical databases. Based on the co-crystal structure of AChE with its ligand galanthamine, a structure-based pharmacophore model was generated and used for an in silico screening of a multi-conformational database consisting of more than 110,000 NPs. From the obtained hit list, promising, virtually active candidates were selected, namely scopoletin (7) and its glucoside scopolin (8) . doi = 10.1007/978-3-7643-8117-2_6 id = cord-292483-u0ycqelc author = Rossmann, Michael G. title = Future prospects date = 2011-04-16 keywords = cryo; structure summary = doi = 10.1016/b978-0-12-386507-6.00005-1 id = cord-264489-h1n9ywbd author = Roy, Urmi title = Insight into the Structures of Interleukin-18 Systems date = 2020-07-31 keywords = IL-18; Roy; structure summary = The present study, including structural and molecular dynamics simulations, takes a close look at the structural stabilities of IL-18 and IL-18 receptor-bound ligand structures as functions of time. The results help to identify the conformational changes of the ligand due to receptor binding, as well as the structural orders of the apo and holo IL-18 protein complexes. This investigative approach assists in the proper identifications of therapeutic-targets, their structural-assemblies and consistent ligand-receptor interfacial interactions, and thus, plays a vital role in the development of new, innovative medicines (Freudenberg et al. The present simulation study examines the structural stabilities of the ligand-protein, IL-18 and IL-18 receptor (IL-18R) bound ligand structures as functions of time. We analyze here the conformational changes within the ligand-protein, due to receptor binding and, we also identify the possible structurally ordered and disordered region within the apo and holo (ligand-bound) protein complexes. doi = 10.1016/j.compbiolchem.2020.107353 id = cord-292985-w62xaa4f author = Römer, Rudolf A. title = Flexibility and mobility of SARS-CoV-2-related protein structures date = 2020-07-12 keywords = SARS; protein; structure summary = We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. 34 We have performed our analysis through multiple conformational steps starting from the crystal structures of SARS-CoV-2-related proteins as currently deposited in the PDB. In Fig. 1 (a) we see that for the crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (PDB:6m3m), the largest rigid cluster in the pristine structure, i.e. at E cut = 0, largely remains rigid through the dilution process of consecutively lowering E cut values. Last, a protein with 2nd-order rigidity should have the most complex behaviour in terms of flexibility since new possible mobility can be expected throughout the range of E cut values. Moving along directions proposed by an elastic normal model analysis of the crystal structure, we can therefore construct possible motion trajectories that are fully consistent with the bond network and steric constraints. doi = 10.1101/2020.07.12.199364 id = cord-023726-2fduzqyb author = STRAUSS, JAMES H. title = The Structure of Viruses date = 2012-07-27 keywords = Fig; RNA; protein; structure; virus summary = Also shown for each family is the presence or absence of an envelope in the virion, the triangulation number (defined later) if the virus is icosahedral, the morphology of the nucleocapsid or core, and figure numbers where the structures of members of a family are illustrated. Structural studies of viruses have shown that the capsid proteins that form the virions of many plant and animal icosahedral viruses have a common fold. The largest particle is the nucleocapsid of herpes simplex virus, which is 1250 Å in diameter and has T=16 symmetry (the virion is enveloped but only the nucleocapsid is regular FIGURE 2.5 Gallery of three-dimensional reconstructions of icosahedral viruses from cryoelectron micrographs. For most RNA viruses, nucleocapsids can be recognized as distinct structures within the infected cell and can be isolated from virions by treatment with detergents that dissolve the envelope. doi = 10.1016/b978-0-12-373741-0.50005-2 id = cord-251982-vbchjexm author = Sarikavak-Lisesivdin, B. title = Structural parameters and electronic properties of 2D carbon allotrope: graphene with a kagome lattice structure date = 2020-09-17 keywords = kagome; structure summary = doi = 10.1016/j.cplett.2020.138006 id = cord-270587-k56fze59 author = Scherbinina, Sofya I. title = Three-Dimensional Structures of Carbohydrates and Where to Find Them date = 2020-10-18 keywords = Bank; Carbohydrate; Data; NMR; PDB; Protein; figure; structure summary = • Database can be freely accessed through web user interface; • Database must contain experimentally confirmed and/or predicted 3D structures (preprocessed and/or generated on-the-fly from a primary structure input) of glycans, glycoproteins, or protein-carbohydrate complexes; • Stored 3D structures must be deposited as atomic coordinates in PDB, MOL, or other format, and the structures must contain a saccharide moiety; • • Database can be freely accessed through web user interface; • Database must contain experimentally confirmed and/or predicted 3D structures (preprocessed and/or generated on-the-fly from a primary structure input) of glycans, glycoproteins, or protein-carbohydrate complexes; • Stored 3D structures must be deposited as atomic coordinates in PDB, MOL, or other format, and the structures must contain a saccharide moiety; • Currently, CHARMM36 parameterization features include monosaccharides in furanose [171] and pyranose [172] forms, glycosidic linkages between monosaccharides [171, 173] , complex carbohydrates and glycoproteins Detailed comparisons of all-chemical and dedicated force fields in a context of glycan modeling have been published [114, 139, 151, 167] . doi = 10.3390/ijms21207702 id = cord-000822-iuglkdcp author = Sperschneider, Jana title = Predicting pseudoknotted structures across two RNA sequences date = 2012-12-01 keywords = RNA; Seq; structure summary = One strong point of the DotKnot method for single sequence pseudoknot prediction (Sperschneider and Datta, 2010; Sperschneider et al., 2011) is that the set of possible H-type pseudoknot candidates (and secondary structure elements) is explicitly computed and thus readily available for further investigation. (3) Use significant pairs to calculate the set of conserved structure elements and pseudoknots for the two sequences that maximizes a combined free energy and similarity score. The key point of the DotKnot-PW approach is how to score the similarity of stems, secondary structure elements and H-type pseudoknot candidates derived from sequences Seq x and Seq y . The optimal structure element alignment, which preserves the interval ordering includes structure elements p 1 , p 4 , p 7 in the first sequence and p 1 , p 4 , p 6 in the second sequence pairwise prediction with highest combined free energy and similarity score is taken, DotKnot-PW has an improved average MCC of 0.81. doi = 10.1093/bioinformatics/bts575 id = cord-103823-3rchp9yy author = Taufer, Michela title = RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology date = 2008-11-30 keywords = Fig; Pknots; RNA; secondary; structure summary = doi = 10.1016/j.parco.2008.08.002 id = cord-301827-a7hnuxy5 author = Uversky, Vladimir N title = A decade and a half of protein intrinsic disorder: Biology still waits for physics date = 2013-04-29 keywords = IDPs; bind; disorder; function; interaction; intrinsic; protein; region; sequence; structure summary = 94 Therefore, the abundance and peculiarities of the charged residues distribution within the protein sequences might determine physical and biological properties of extended IDPs and IDPRs. Also, simple polymer physics-based reasoning can give reasonably well-justified explanation of the conformational behavior of extended IDPs. In general, the conformational behavior of IDPs is characterized by the low cooperativity (or the complete lack thereof) of the denaturant-induced unfolding, lack of the measurable excess heat absorption peak(s) characteristic for the melting of ordered proteins, "turned out" response to heat and changes in pH, and the ability to gain structure in the presence of various binding partners. 183 This analysis revealed that proteins involved in regulation and execution of PCD possess substantial amount of intrinsic disorder and IDPRs were implemented in a number of crucial functions, such as protein-protein interactions, interactions with other partners including nucleic acids and other ligands, were shown to be enriched in post-translational modification sites, and were characterized by specific evolutionary patterns. doi = 10.1002/pro.2261 id = cord-310847-63gh2tg4 author = Uversky, Vladimir N title = The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins date = 2013-04-01 keywords = Glu; PGA; acid; domain; glutamic; protein; region; residue; rich; structure summary = 5, 10, 46 In fact, in comparison with ordered proteins, IDPs/IDPRs are characterized by noticeable biases in their amino acid compositions, 5, 8, 10, [46] [47] [48] containing less of so-called "order-promoting" residues (cysteine, tryptophan, isoleucine, tyrosine, phenylalanine, leucine, histidine, valine, asparagines and methionine, which are mostly hydrophobic residues which are commonly found within the hydrophobic cores of foldable proteins) and more of "disorder-promoting" residues (lysine, glutamine, serine, glutamic acid and proline, which are mostly polar and charged residues, which are typically located at the surface of foldable proteins) (Fig. 1A) . Glutamic acid is an important functional residue of ordered proteins, where it can be involved in the formation of specific electrostatic valves inside the pores of ion channels, or can play unique catalytic roles in the active sites doi = 10.4161/idp.24684 id = cord-324410-be2ith3z author = Wang, Qi title = Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry date = 2007-06-13 keywords = EUDOC; crystal; structure summary = These results demonstrate the significant influence of crystal packing on small molecule complexation and suggest that EUDOC is able to predict small-molecule complexes and that it is useful for the design of new materials, molecular sensors, and multimeric inhibitors of protein-protein interactions. To expand the application of the EUDOC program to supramolecular chemistry, we tested its ability to reproduce the crystal structures of small-molecule guest-host complexes. Herein we report the results of our docking studies with 161 selected crystal structures of small-molecule guest-host complexes using the EUDOC program. These results show that the program is able to reproduce all 161 crystal structures and that the average interaction energy of these small-molecule complexes (250.1 kcal/mol) is nearly half of that of the 153 small molecule-bound protein complexes we studied in previous tests (2108.5 kcal/mol). The results also demonstrate the significant influence of crystal packing on small-molecule complex crystal structures and suggest that the EUDOC program is able to predict 3D structures of small-molecule guest-host complexes with reasonable reliability. doi = 10.1371/journal.pone.0000531 id = cord-022494-d66rz6dc author = Webb, B. title = Comparative Modeling of Drug Target Proteins date = 2014-10-01 keywords = comparative; model; modeling; sequence; structure summary = doi = 10.1016/b978-0-12-409547-2.11133-3 id = cord-314329-rzda8x62 author = Wells, Stephen A. title = Rigidity, normal modes and flexible motion of a SARS-CoV-2 (COVID-19) protease structure date = 2020-03-12 keywords = PDB; motion; structure summary = doi = 10.1101/2020.03.10.986190 id = cord-287450-hydy874v author = Wendt, K Ulrich title = Structures and diseases date = 2008 keywords = Institute; University; protein; structure summary = In early September 2007, about 180 structural biologists and biochemists met in the picturesque town of Murnau, located near Staffelsee Lake in the Bavarian alpine upland, to reflect on these questions and discuss recent biostructural data on the molecular determinants of human diseases, including microbial and viral infections, protein misfolding diseases, cancer and metabolic disorders. Starting the session on viral diseases, Rolf Hilgenfeld (University of Lübeck) reviewed the work from his laboratory on proteases of RNA viruses, such as severe acute respiratory syndrome (SARS) coronavirus and coxsackievirus B3, and also highlighted recent structural data on falcipain-2 from Plasmodium falciparum, discussing implications for the design of active-site directed and allosteric inhibitors for these cysteine proteases 14 . Günter Fritz (University of Konstanz) presented the unpublished structure of the ligand binding domain of RAGE, a multiligand receptor for advanced glycation end products, S100 proteins, HMGB1 and amyloid-β, whose activation is key to numerous chronic diseases such as diabetes, inflammation, arteriosclerosis and neurodegeneration, making it a potential therapeutic target 32, 33 . doi = 10.1038/nsmb0208-117 id = cord-313694-p2sgaypq author = West, Christopher M. title = Current ideas on the significance of protein glycosylation date = 1986 keywords = Golgi; carbohydrate; cell; glycoprotein; protein; structure summary = The alternate view is that carbohydrate structures participate in numerous specific interactions with discrete protein receptors, and that these interactions lead to predictable modifications in the localization or activity of the glycoprotein. The notion of a ''non-specific'' role for carbohydrate has received perhaps its strongest support from studies on cells whose glycosylation processes have been globally altered by mutation or drugs. Consideration of the possible role of carbohydrate in other molecular associations with the plasma membrane will be considered below in sections on hormone-receptor interactions and cellsubstratum (e.g., extracellular matrix) and cell-cell adhesion. Considerable evidence has been adduced that various parasites such as viruses, bacteria, protozoa, etc., possess carbohydrate binding proteins which can interact with sugar structures on the surfaces of cells with which the parasites associate (167, 168, (116) (117) (118) (119) . In any case, antibodies and lectins may model potential receptors in cells which might specifically recognize carbohydrate-associated structures. doi = 10.1007/bf00230632 id = cord-349839-s32d3di2 author = Westhof, Eric title = RNA pseudoknots date = 1992-06-30 keywords = RNA; Structure; pseudoknot summary = In the folding of a single-stranded RNA molecule, there are only three ways in which two base-paired segments can be related to each other: two consecutive hairpins; two helices separated by an internal bulge; and, pseudoknots [1]. The first two motifs can be represented as two-dimensional graphs without self-intersections whereas pseudoknots cannot, as they are fundamentally three-dimensional structures in which the four base-paired strands alternate along the sequence of the RNA molecule. The three types of ''classic'' pseudoknots with co-axial stacking of the two base-paired helices and with single-stranded segments crossing the RNA grooves. The third pseudoknot involves the 530 stem-loop structure [19] , which is known to be important for the binding of tRNA to the ribosomal A site [20] , and was recently shown to be essential for ribosomal function [21.o] . doi = 10.1016/0959-440x(92)90221-r id = cord-263017-rh86g4jk author = Wigginton, Krista Rule title = Virus disinfection mechanisms: the role of virus composition, structure, and function date = 2011-12-09 keywords = inactivation; structure; virus summary = Non-culturable virus disinfection kinetics must be either determined with human charge studies or predicted using surrogate viruses that can be cultured in vitro but that differ in composition, structure, and function. Coupling structure and composition information aids in our understanding of virus reactivity X-ray crystal structures have been published for numerous enteric viruses [25,26 ,27] and with these reports have come a windfall of valuable information including the location and orientation of capsid protein residues. Specific questions include: 1) Which virus protein residues are involved with fundamental functions and how do these vary amongst different strains and species; 2) What specific chemical modifications take place in the genome and capsid during disinfection and what effects do these modifications have on virus structure and function; 3) How similar are disinfectant-induced modifications amongst various enteric viruses? doi = 10.1016/j.coviro.2011.11.003 id = cord-266921-x9q7dwc4 author = Worrall, Jonathan AR title = Information available at cut rates: structure and mechanism of ribonucleases date = 2006-12-26 keywords = RNA; RNase; figure; structure summary = The exoribonuclease RNase II is representative of an extensive enzyme family found in all three domains of life, whose members play roles in the maturation, turn-Structure and mechanism of ribonucleases Worrall and Luisi 131 Whereas DEAD-box helicases use the free energy of ATP binding and hydrolysis to disrupt secondary structure, RNase R transduces the favourable free energy of RNA backbone hydrolysis into mechanical work that translates the single-stranded substrate further into the catalytic pocket, much like a ratchet. Crystal structures of the core of the exosomes from the archaea Sulfolobus solfataricus and Archaeoglobus fulgidus have recently become available, revealing a hexameric ring comprising two types of RNase-PH-like subunits, known as Rrp41 and Rrp42 (rRNA-processing proteins 41 and 42; see Figure 4a ) [36 ,37 ,38 ] . Structure of Escherichia coli RNase E catalytic domain and its implications for RNA turnover and processing doi = 10.1016/j.sbi.2006.12.001 id = cord-018963-2lia97db author = Xu, Ying title = Protein Structure Prediction by Protein Threading date = 2010-04-29 keywords = fold; protein; sequence; structure; threading summary = Their follow-up work (Elofsson et aI., 1996; Fischer and Eisenberg, 1996; Fischer et aI., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et aI., 1992) on protein fold recognition led to the development of a new brand ofpowerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many ofthe proteins encoded in the hundreds of genomes that have been sequenced up to now. doi = 10.1007/978-0-387-68825-1_1 id = cord-340554-7cwp2xbw author = Yamasaki, Satoshi title = ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow date = 2019-03-06 keywords = RNA; Rascal; structure; tertiary; workflow summary = The tertiary structure of RNA molecules and RNA–RNA/protein interaction sites are of increasing importance as potential targets for new medicines that treat a broad array of human diseases. In this report, we present a novel workflow to predict RNA tertiary structures and RNA–RNA/protein interactions using the KNIME environment, which enabled us to assemble a combination of RNA-related analytical tools and databases. The workflow, RNA Structure Prediction, at the top of Fig. 1 models the tertiary structure of the RNA target according to secondary structure information, which is based on the calculated results from CentroidFold [36] . Figure 2c , d show the predicted secondary and tertiary structures for the non-coding RNA (FR000373 of fRNAdb) calculated by the CentroidFold and Rascal nodes. The RNA-protein workflow is presented at the bottom of Fig. 1 and is used to predict the structure of a nucleic acid drug-target protein complex by molecular simulations. doi = 10.1007/s10822-019-00195-y id = cord-319906-s7kzp795 author = Zemla, Adam T title = StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase date = 2011-06-02 keywords = RNA; figure; residue; structure summary = When for a given reference structure a structure-based search is performed on a set of proteins from the Protein Data Bank (PDB), StralSV identifies all structurally similar fragments from that set, evaluates the calculated structure-based alignments between the query (reference) motif (designated "segment" in this work) and the detected structure fragments, and quantifies the observed sequence variability at each residue position on the query structure. (For an illustration of a "span", see additional file 1: StralSV-RdRp_Suppl_Figure 1.docx.) All residue-residue pairs that are contained within a span''s alignment are used to calculate the sequence variability data at the corresponding position in the query structure. The qualified hits (structure fragments from PDB with detected local similarities to the query structure) for six selected sequence positions (positional hits) of polio RdRp (positions identified in Figure 3 ) were categorized and quantified based on SCOP (Structure Classification of Proteins database; version 1.75, June 2009 release) identifiers [32] . doi = 10.1186/1471-2105-12-226 id = cord-310192-8x37nx4s author = Zhang, Huaqun title = Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy date = 2019-04-25 keywords = NMR; RNA; large; structure summary = doi = 10.1002/wrna.1541 id = cord-312946-p2iazl7z author = Ziółkowska, Natasza E. title = Domain-Swapped Structure of the Potent Antiviral Protein Griffithsin and Its Mode of Carbohydrate Binding date = 2006-07-18 keywords = griffithsin; structure summary = The crystal structure of griffithsin, an antiviral lectin from the red alga Griffithsia sp., was solved and refined at 1.3 Å resolution for the free protein and 0.94 Å for a complex with mannose. Antiviral potency of griffithsin is likely due to the presence of multiple, similar sugar binding sites that provide redundant attachment points for complex carbohydrate molecules present on viral envelopes. Another conserved broad loop with the GGSGG sequence, 86-90, is located near the secondary carbohydrate binding site in calsepa and follows a course quite different than in banana and parkia lectins, yet similar to the path in the other proteins. The second crystal form, grown from material expressed in plants and containing only 121 residues in a protein chain, was orthorhombic (P2 1 2 1 2 1 ) and contained two griffithsin molecules in the asymmetric unit. doi = 10.1016/j.str.2006.05.017 id = cord-031957-df4luh5v author = dos Santos-Silva, Carlos André title = Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era date = 2020-09-02 keywords = amp; antimicrobial; figure; model; peptide; pin; plant; protein; sequence; structure summary = 19 Plant AMPs are the central focus of the present review, comprising information on their structural features (at genomic, gene, and protein levels), resources, and bioinformatic tools available, besides the proposition of an annotation routine. 26 Plant AMPs are also classified into families considering protein sequence similarity, cysteine motifs, and distinctive patterns of disulfide bonds, which determine the folding of the tertiary structure. 27, 31 These AMP categories will be detailed in the next sections, together with other groups here considered (Impatienlike, Macadamia [β-barrelins], Puroindoline (PIN), and Thaumatin-like protein [TLP]) and the recently described αhairpinin AMPs. The description includes comments on their structure, pattern for regular expression (REGEX) analysis (when available), functions, tissue-specificity, and scientific data availability. 179 As to the TLP structure, this protein presents characteristic thaumatin signature (PS00316): 180, 181 Most of the TLPs have molecular mass ranging from 21 to 26 kDa, 163 possessing 16 conserved cysteine residues (Supplementary Figure S8) involved in the formation of 8 disulfide bonds, 182 which help in the stability of the molecule, allowing a correct folding even under extreme conditions of temperature and pH. doi = 10.1177/1177932220952739 id = cord-001835-0s7ok4uw author = nan title = Abstracts of the 29th Annual Symposium of The Protein Society date = 2015-10-01 keywords = ATP; Biology; Ca21; Chemistry; Department; Institute; NADPH; NMR; PDB; RNA; Science; Tau; University; activity; base; bind; binding; cell; change; complex; design; dna; domain; enzyme; form; function; high; interaction; membrane; method; molecular; peptide; process; protein; residue; result; role; sequence; site; structure; study summary = Altogether, these results indicate that, although PHDs might be more selective for HIF as a substrate as it was initially thought, the enzymatic activity of the prolyl hydroxylases is possibly influenced by a number of other proteins that can directly bind to PHDs. Non-natural aminoacids via the MIO-enzyme toolkit Alina Filip 1 , Judith H Bartha-V ari 1 , Gergely B an oczy 2 , L aszl o Poppe 2 , Csaba Paizs 1 , Florin-Dan Irimie 1 1 Biocatalysis and Biotransformation Research Group, Department of Chemistry, UBB, 2 Department of Organic Chemistry and Technology An attractive enzymatic route to enantiomerically pure to the highly valuable a-or b-aromatic amino acids involves the use of aromatic ammonia lyases (ALs) and aminomutases (AMs). Continuing our studies of the effect of like-charged residues on protein-folding mechanisms, in this work, we investigated, by means of NMR spectroscopy and molecular-dynamics simulations, two short fragments of the human Pin1 WW domain [hPin1(14-24); hPin1(15-23)] and one single point mutation system derived from hPin1(14-24) in which the original charged residues were replaced with non-polar alanine residues. doi = 10.1002/pro.2823 id = cord-004534-jqm1hxps author = nan title = Abstract date = 2009-06-09 keywords = AFM; ATP; Biology; Biophysics; Chemistry; Department; FCS; France; GFP; Genova; Germany; Hyp; Institute; Italy; Molecular; Physics; RNA; Sciences; University; cell; dna; fluorescence; fret; interaction; lipid; membrane; protein; result; structure; study summary = HIV-1 to efficiently complete a replication cycle has to integrate its genome into the host cellular DNA.After HIV-1 enters target cells,neosynthesized viral DNA forms along with other proteins the pre-integration complex (PIC).PICs are then transported into the nucleus where integration,catalyzed by the viral integrase,takes place.HIV-1 viral particles engineered to incorporate integrase fused to EGFP have proven effective to study PICs within nuclei of infected cells.In this study we report the live imaging analysis of nuclear PIC dynamics obtained by time-lapse microscopy.Intranuclear trajectories of IN-EGFP-labeled PIC were collected in three dimensions and examined by both mean squared displacement (MSD) and cage diameter (CD) analysis.In CD the maximum distances measured between two positions occupied by a PIC in a time window of 2 minutes were calculated while in our MSD analysis 5-minute long trajectory segments were considered.Remarkably,MSD revealed the presence of an underlying active transport mechanism.To test the possible role of actin filaments,PIC nuclear trafficking was analyzed in cells treated with latrunculin B (actin polymerization inhibitor).Preliminary results suggest that the disruption of actin function impairs the active nuclear movement of PICs. Second harmonic generation microscopy reveals sarcomere contractile dynamics of cardiomyocytes N. doi = 10.1007/s00249-009-0478-1 id = cord-004584-bcw90f5b author = nan title = Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date = 2011-08-06 keywords = AFM; ATP; Biophysics; Department; FCS; Germany; Institute; RNA; University; cell; change; channel; complex; different; dna; dynamic; effect; fluorescence; fret; high; interaction; lipid; mechanism; membrane; model; molecular; molecule; process; protein; result; structure; study; surface; system summary = doi = 10.1007/s00249-011-0734-z id = cord-014685-ihh30q6f author = nan title = Posters P788 - P999 date = 2005-09-21 keywords = Department; France; Institute; Japan; RNA; University; cell; dna; membrane; protein; structure; study summary = This study has attempted to analyse the structural properties of membrane peptides and proteins through the use of model systems that have been designed to mimic their natural counterparts: Podlubnaya 2 1 Institute of Theoretical and Experimental Biophysics RAS, 2 Pushchino State University Amyloid brils are formed by proteins or their peptides in the result of a conformational transition from alpha helix into beta-sheet structure. Analysis of the results of such studies indicate that folding of SNase fragments is dominated by developing the local and non-local nucleation sites from native-like secondary structures and by intensifying the longrange interactions of residues at nucleation sites with residues further removed in sequence. The results show that at different pH values the aggregation processes of both proteins follow different pathways determined by the variations in the native structure and by the details of the involved conformational changes. doi = 10.1007/s00249-005-0504-x id = cord-015619-msicix98 author = nan title = Virus Structure & Assembly date = 2009-02-24 keywords = SARS; dna; structure; virus summary = The studies were performed with nanoindentation techniques using an Atomic Force Microscope (AFM), an approach which is becoming a standard method to measure the mechanical properties of viral particles (1, 2) . Using molecular dynamics simulations of the connector in complex with DNA, and aiming at distinguishing between these three models, we calculated mechanical properties of this system. The bacteriophage lambda is composed of an icosahedral capsid, into which a 48.5 kbp double-stranded DNA genome is packaged, and a long non-contractile tail consisting of 34 disk-like structures. The relative probabilities of fusion and endocytosis of a virus particle initially nonspecifically adsorbed on the host cell membrane are computed as functions of receptor concentration, binding strength, and number of spikes. As revealed by techniques of structural biology and single-molecule experimentation, the capsids of viruses are some of nature''s best examples of highly symmetric multiscale self-assembled structures with impressive mechanical properties of strength and elasticity. doi = 10.1016/s0006-3495(08)79065-9 id = cord-023208-w99gc5nx author = nan title = Poster Presentation Abstracts date = 2006-09-01 keywords = Fmoc; Gly; HPLC; Lys; NH2; NMR; Pro; RGD; RNA; Tyr; acid; activity; amino; bind; cell; dna; high; interaction; method; peptide; protein; receptor; result; sequence; structure; study summary = In order to develop a synthetic protocol by an automated instrumentation, increasing yield, purity of the crude, and reaction time, a microwave-assisted solid phase peptide synthesis was validated comparing the use of the new generation of Triazine-Based Coupling Reagents (TBCRs) with a series of commonly used ones. Ubiquitinium is a well known mechanism in protein degredation of Eukaryotic cells ,in which many obsolte and corrupted three dimentional structure protein ,become marked by covalent attachment of ubuquitin through a multi-step enzymatic pathway.Ubiquitin is a small ,8.5 kDa peptide of 76 amino acid residues that targets such substrtes for proteolysis in proteasome .Recnt studies showed that an extra cellular ubiquitination process also taking place in the epididymes of humans and other animals marks protein on the surface of the defective sperm .it appears that structurally and functionally defective sperm become surface ubiquitinated by epididymal epithelial cells. This head-to-tailcyclized 14-amino-acid peptide contains one disulfide bridge and a lysine residue (Lys5) present in the P1 position, which is responsible for inhibitor specificity.As was reported by us and other groups, SFTI-1 analogues with one cycle only retain trypsin inhibitory activity. doi = 10.1002/psc.797 id = cord-023209-un2ysc2v author = nan title = Poster Presentations date = 2008-10-07 keywords = Ala; Arg; Asp; Fmoc; Glu; Gly; HPLC; Leu; Lys; NMR; Phe; Thr; Trp; Tyr; University; VEGF; Val; acid; activity; amino; bind; cell; dna; high; peptide; pro; protein; receptor; residue; result; sequence; structure; study; synthesis summary = Site-specifi c PEGylation of human IgG1-Fab using a rationally designed trypsin variant In the present contribution we report on a novel, highly selective biocatalytic method enabling C-terminal modifi cations of proteins with artifi cial functionalities under native state conditions. Recently, our group report a novel approach to a totally synthetic vaccine which consists of FMDV (Foot and Mouth Disease Virus) VP1 peptides, prepared by covalent conjugation of peptide biomolecules with membrane active carbochain polyelectrolytes In the present study, peptide epitops of VP1 protein both 135-161(P1) amino acid residues (Ser-Lys-Tyr-Ser-Thr-Thr-Gly-Glu-Arg-Thr-Arg-Thr-Arg-Gly-Asp-Leu-Gly-Ala-Leu-Ala-Ala-Arg-Val-Ala-Thr-Gln-Leu-Pro-Ala) and triptophan (Trp) containing on the N terminus 135-161 amino acid residues (Trp-135-161) (P2) were synthesized by using the microwave assisted solid-phase methods. Using as a template a peptide, already identifi ed, with agonist activity against PTPRJ(H-[Cys-His-His-Asn-Leu-Thr-His-Ala-Cys]-OH), here we report a structure-activity study carried out through endocyclic modifi cations (Ala-scan, D-substitutions, single residue deletions, substitutions of the disulfi de bridge) and the preliminary biological results of this set of compounds. doi = 10.1002/psc.1090 id = cord-023225-5quigar4 author = nan title = Posters date = 2012-08-21 keywords = Aib; Ang; Cys; Fmoc; Gly; HPLC; Ile; Leu; Lys; NMR; PNA; Phe; SPPS; University; acid; activity; amino; cell; dna; group; peptide; protein; residue; structure; study; synthesis summary = To further explore the structure-function relationship, a viable synthesis strategy for pseudodesmin A analogues was developed, based on side-chain attachment of the first amino acid to the solid support, followed by stepwise Fmoc solid-phase synthesis of the linear peptide precursor and on-resin head-to-tail cyclization. The cases when the amino acid sequence of a fragment coincided with part of the primary structure of a natural oligopeptide were recorded in the Total protein chemical synthesis requires a case by case design and optimization which is governed by factors such as the solubility of the individual peptide segments, their primary sequence and in particular the presence of "difficult" amino acid residues at ligation junctions such as proline or the location of cysteines. In this study we present synthesis of two series of peptide libraries, which were designed by substitution of Leu in the P5, P6 position of our control peptide (Ac-LLLLRVKR-AMBA) with each of nineteen amino acid residues in order to verifying its influence on activity and selectivity of the resulting analogues. doi = 10.1002/psc.2449 id = cord-023284-i0ecxgus author = nan title = Abstracts of publications related to QASR date = 2006-09-19 keywords = Fig; NMR; chemical; compound; datum; model; molecular; result; structure summary = Results: Methods developed for the investigation for the relationships between structure and toxic effects of compounds are summarized: a) The extra-thermodynamic approach: the Hansch paradigm, physical chemical properties that influence biological activity and their parametrization, originality of the Hansch approach, receptors and pharmacophores: the natural content of the Hansch approach, predictive value of QSARs, a statistifa1 tool: multiple linear regression analysis, the problem of correlations among molecular descriptors, other mathematical utilizations of extrathermodynamic parameters; b) The substructural approach: when topological (substructural) descriptors are needed, how to use topological decriptors; c) QSAR in mutagenicity and carcinogenicity: general problems, specific versions of the substructural approach used for mutagenicity and carcinogenicity, applications to mutagenicity and carcinogenicity. doi = 10.1002/qsar.19900090309 id = cord-023442-4vzwc2d2 author = nan title = Proceedings of SCANNING 94/SEEMS 94 Charleston, South Carolina, USA date = 2006-12-05 keywords = Carlo; EPMA; Fig; Monte; Mott; SEM; Scanning; Supplement; TEM; USA; Vol; beam; cell; electron; figure; high; image; microscopy; result; sample; section; specimen; structure; study; surface summary = IV-4 Scanning Vol. 16, Supplement IV (1994) Simulation of image formation and detection systems in the SEM is a vital link in performing image analysis to obtain precise measurements, to provide the necessary connection between image parameters and structural dimensions, and to reflect important microscope beam and detector parameters. By knowing the transfer function, noise, and distortion figure in digital form, it is relatively easy to obtain more accurate comparison of the measured and calculated signal (Fig. 1 The calculation of image contrast in the scanning electron microscope (SEM) can be done using Monte Carlo techniques if the electron trajectories can be calculated through the composition profiles in the specimen. Specimens providing IV-18 Scanning Vol. 16, Supplement IV (1994) FIG highly redundant structures and relatively smooth fractures, such as cell suspensions or o/w emulsions, were investigated using freeze fracture/replication and ambient temperature transmission electron microscopy (AT-TEM). doi = 10.1002/sca.4950160315