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PISCES: recent improvements to a PDB sequence culling server

G. Wang, R. L. Dunbrack
<span title="2005-07-01">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
PISCES now allows a user to cull the PDB by-entry in addition to the standard culling by individual chains.  ...  PISCES is a database server for producing lists of sequences from the Protein Data Bank (PDB) using a number of entry-and chain-specific criteria and mutual sequence identity.  ...  ACKNOWLEDGEMENTS We thank Dr Adrian A. Canutescu for advice on the web server implementation of PISCES.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki402">doi:10.1093/nar/gki402</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15980589">pmid:15980589</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1160163/">pmcid:PMC1160163</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y3t2upw4gbarbb4fugjduhko54">fatcat:y3t2upw4gbarbb4fugjduhko54</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060101025236/http://dunbrack.fccc.edu:80/Guoli/pisces.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/60/1c/601c93859d36a0027d9a31ffee316dfa448b19a7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki402"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160163" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Maximising the Size of Non-Redundant Protein Datasets Using Graph Theory

Simon C. Bull, Mark R. Muldoon, Andrew J. Doig, Anna Tramontano
<span title="2013-02-05">2013</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
From a starting set, such as the PDB or a genome, one should remove as few sequences as possible, to give the largest possible non-redundant set for subsequent analysis.  ...  This is usually achieved by pairwise comparison of sequences, followed by purging so that no two pairs have similarities above a chosen threshold.  ...  The website uses Leaf to cull subsets of the PDB or submitted user sequences.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0055484">doi:10.1371/journal.pone.0055484</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23393584">pmid:23393584</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3564766/">pmcid:PMC3564766</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/naaiirjoovezxmrhe7ur4yig3u">fatcat:naaiirjoovezxmrhe7ur4yig3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171006024639/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0055484&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6b/1d/6b1d87c500b7c3fc4c3423e4efe558f10de19868.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0055484"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564766" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dinosolve: a protein disulfide bonding prediction server using context-based features to enhance prediction accuracy

Ashraf Yaseen, Yaohang Li
<span title="2013-10-01">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Our disulfide prediction algorithm is implemented on a web server named "Dinosolve" available at: http://hpcr.cs.odu.edu/dinosolve.  ...  The mean-force potentials are integrated as context-based scores to estimate the favorability of a cysteine residue in disulfide bonding state as well as a cysteine pair in disulfide bond connectivity.  ...  We also use another dataset Cull7986 generated from PISCES server with maximum 25% sequence identity, 3.0A resolution, and 1.0 R-factor.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s13-s9">doi:10.1186/1471-2105-14-s13-s9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24267383">pmid:24267383</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3849605/">pmcid:PMC3849605</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qvqsxzaktffmvf75aettyqa32a">fatcat:qvqsxzaktffmvf75aettyqa32a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426215620/https://digitalcommons.odu.edu/cgi/viewcontent.cgi?article=1041&amp;context=computerscience_fac_pubs" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/83/25/83254a2a61ef3106c9b093be992afdcbd5c13c96.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s13-s9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849605" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Nh3D: a reference dataset of non-homologous protein structures

B Thiruv, G Quon, S A Saldanha, B Steipe
<span title="2005-07-12">2005</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m36qvjwuvnegpgzopqbhvg7k3e" style="color: black;">BMC Structural Biology</a> </i> &nbsp;
Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB.  ...  The current Nh3D list contains 570 domains with a total of 90780 residues.  ...  Acknowledgements Funding contributions are gratefully acknowledged from the Canadian Institutes of Health Research (operating grant MOP 93075) and from a subgrant within the Genome Canada Competition II  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-5-12">doi:10.1186/1472-6807-5-12</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16011803">pmid:16011803</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1182382/">pmcid:PMC1182382</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/22knkdewbnezdn65b2fiwmbatu">fatcat:22knkdewbnezdn65b2fiwmbatu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428170332/https://bmcstructbiol.biomedcentral.com/track/pdf/10.1186/1472-6807-5-12" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/73/df/73df18e209d47a59e3bb2b2520c3d89d303b69d5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-5-12"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182382" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DSP: a protein shape string and its profile prediction server

J. Sun, S. Tang, W. Xiong, P. Cong, T. Li
<span title="2012-05-02">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
To fill this gap, we have developed an accurate shape string predictor based on two innovative technologies: a knowledge-driven sequence alignment and a sequence shape string profile method.  ...  The DSP server provides both predicted shape string and sequence shape string profile for each query sequence.  ...  ACKNOWLEDGEMENTS The authors are grateful to the anonymous reviewers for their valuable comments and help in improving the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks361">doi:10.1093/nar/gks361</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22553364">pmid:22553364</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3394270/">pmcid:PMC3394270</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hazdfbex4veexexxpgkz7jooia">fatcat:hazdfbex4veexexxpgkz7jooia</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226140219/http://pdfs.semanticscholar.org/6e28/b2654727abaa0e4cdd3ddcaddcabbd930279.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6e/28/6e28b2654727abaa0e4cdd3ddcaddcabbd930279.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks361"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394270" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Superimpose: a 3D structural superposition server

R. A. Bauer, P. E. Bourne, A. Formella, C. Frommel, C. Gille, A. Goede, A. Guerler, A. Hoppe, E.-W. Knapp, T. Poschel, B. Wittig, V. Ziegler (+1 others)
<span title="2008-05-19">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
After the computation on our server infrastructure, a visual assessment of the results is provided.  ...  The Superimposé server is available at:  ...  ACKNOWLEDGEMENTS We thank Yang Zhang for the permission to use TM-align on the Superimpose´server and also Igor Filippov, Marc C.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn285">doi:10.1093/nar/gkn285</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18492720">pmid:18492720</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2447795/">pmcid:PMC2447795</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c7ljn4uj6fbsxmmu4qfcwdirqi">fatcat:c7ljn4uj6fbsxmmu4qfcwdirqi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220231229/http://pdfs.semanticscholar.org/2ad0/bf6adcbe153b6d774cde708eb521a9623c8e.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2a/d0/2ad0bf6adcbe153b6d774cde708eb521a9623c8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn285"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447795" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A series of PDB related databases for everyday needs

R. P. Joosten, T. A. H. te Beek, E. Krieger, M. L. Hekkelman, R. W. W. Hooft, R. Schneider, C. Sander, G. Vriend
<span title="2010-11-11">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems.  ...  The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB.  ...  The EU contributed in the 90 0 s to the initial design of several of the systems mentioned. More recent financial support came also from EMBRACE, BioSapiens, Elixir and NBIC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq1105">doi:10.1093/nar/gkq1105</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21071423">pmid:21071423</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3013697/">pmcid:PMC3013697</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jl2ocrg3v5avbgz7cdxbs3rsie">fatcat:jl2ocrg3v5avbgz7cdxbs3rsie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210801043906/https://repository.ubn.ru.nl/bitstream/handle/2066/91525/1/91525.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/76/0d/760da7a8494f16b3f31153e3be93461145e037a0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq1105"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013697" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

Bent Petersen, Claus Lundegaard, Thomas Nordahl Petersen, Andreas Hofmann
<span title="2010-11-30">2010</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
In the present work, neural network methods have been trained to predict b-turn or not and individual b-turn types from the primary amino acid sequence.  ...  The performance is evaluated using a golden set of non-homologous sequences known as BT426.  ...  Acknowledgments We would like to thank Ramneek Gupta with his help to proofread this manuscript. Author Contributions Conceived and designed the experiments: BP CL TNP.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0015079">doi:10.1371/journal.pone.0015079</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21152409">pmid:21152409</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2994801/">pmcid:PMC2994801</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yi4g75qldbfljjlitp3myvup6y">fatcat:yi4g75qldbfljjlitp3myvup6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170927025718/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0015079&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/00/34/0034ed6e50b9e3711b6ce813850969eba055ed27.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0015079"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994801" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

LYRA, a webserver for lymphocyte receptor structural modeling

Michael Schantz Klausen, Mads Valdemar Anderson, Martin Closter Jespersen, Morten Nielsen, Paolo Marcatili
<span title="2015-05-24">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Template database PDB codes of all BCR and TCR structures present in the IMGT/3Dstructure-DB (16) were retrieved and culled using the Pisces web server (17) to remove all redundant structures.  ...  Case study To demonstrate the functionality of the LYRA web server also for TCR modeling, we show the modeling of 4×6B (40), a TCR molecule recently published in the PDB database and with a sequence similarity  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv535">doi:10.1093/nar/gkv535</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26007650">pmid:26007650</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4489227/">pmcid:PMC4489227</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/immgjruugfhcjes3nidvckfiuu">fatcat:immgjruugfhcjes3nidvckfiuu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723091053/http://orbit.dtu.dk/files/112337807/LYRA.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/7a/ac7aab69b9c1c9eab9d14fba22b609b48841c978.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv535"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489227" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A generic method for assignment of reliability scores applied to solvent accessibility predictions

Bent Petersen, Thomas Petersen, Pernille Andersen, Morten Nielsen, Claus Lundegaard
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m36qvjwuvnegpgzopqbhvg7k3e" style="color: black;">BMC Structural Biology</a> </i> &nbsp;
Acknowledgements We would like to thank Associate professor Thomas Blicher with his help to proofread this manuscript.  ...  For training of the method, a dataset, was downloaded from the PISCES server [29] on July 10th 2004 and consisted of 2,085 sequences with sequence identity <25%, Resolution < 2.0 Å and R-factor < 0.25  ...  server PISCES [29] available at http://dun brack.fccc.edu/PISCES.php.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-9-51">doi:10.1186/1472-6807-9-51</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19646261">pmid:19646261</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2725087/">pmcid:PMC2725087</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rg2ojacydfgn5hwfjcojkkjfjm">fatcat:rg2ojacydfgn5hwfjcojkkjfjm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190418083918/https://core.ac.uk/download/pdf/13749044.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/b2/efb2051fa5dcf186aefca1720572bc6a624516d9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-9-51"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725087" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Charge environments around phosphorylation sites in proteins

James Kitchen, Rebecca E Saunders, Jim Warwicker
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m36qvjwuvnegpgzopqbhvg7k3e" style="color: black;">BMC Structural Biology</a> </i> &nbsp;
Phosphorylation is a central feature in many biological processes.  ...  Structural analyses have identified the importance of charge-charge interactions, for example mediating phosphorylation-driven allosteric change and protein binding to phosphopeptides.  ...  Acknowledgements This work was funded by a UK BBSRC studentship to JK. We thank Mr Stephen Hall and Dr Nick Gresham for technical support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-8-19">doi:10.1186/1472-6807-8-19</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18366741">pmid:18366741</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2291461/">pmcid:PMC2291461</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yvmmu26yqnccjcoa343yngmiwy">fatcat:yvmmu26yqnccjcoa343yngmiwy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171002193825/https://core.ac.uk/download/pdf/1383923.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fa/51/fa51a92758d9e01621c691c3ffc1b17e4fdbe7f3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1472-6807-8-19"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2291461" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Facilities that make the PDB data collection more powerful

Joanna Lange, Coos Baakman, Arthur Pistorius, Elmar Krieger, Rob Hooft, Robbie Joosten, Gert Vriend
<span title="2019-11-14">2019</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
The VASE software has been added to analyze and visualize HSSP multiple sequence alignments for protein structures.  ...  The PDB-REDO collection of reanalyzed and re-refined protein structures that were solved by X-ray crystallography has been improved by dealing better with sugar residues and with hydrogen bonds, and adding  ...  ACKNOWLEDGEMENTS We are thankful to Roman Laskowski, Henning Hermjakob, and many other EBI staff for useful advice.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.3788">doi:10.1002/pro.3788</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31724231">pmid:31724231</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6933850/">pmcid:PMC6933850</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/reit6vqsyrfmnakgeuemjy3xpy">fatcat:reit6vqsyrfmnakgeuemjy3xpy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200502103054/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6933850&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7a/fc/7afcd4189cdb2f73dc368a90b75b0b6ff9f98b56.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.3788"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6933850" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A METHOD TO PREDICT EDGE STRANDS IN BETA-SHEETS FROM PROTEIN SEQUENCES

Antonin Guilloux, Bernard Caudron, Jean-Luc Jestin
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cmflnsn2l5gylcviv447te3mku" style="color: black;">Computational and Structural Biotechnology Journal</a> </i> &nbsp;
Citation Guilloux A, Caudron B, Jean-Luc Jestin JL (2013) A method to predict edge strands in beta-sheets from protein sequences.  ...  Abbreviations x and Yare velocities; m and M are respectively the masses of the folding unit and of the folding entity after the folding step; PDB is the Protein Data Bank; SOF is a Sequence Optimized  ...  The second test set with proteins chosen according to different functions and organisms was then analyzed by looking for potential sequence homology using the culling server Pisces [47] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5936/csbj.201305001">doi:10.5936/csbj.201305001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24688737">pmid:24688737</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3962219/">pmcid:PMC3962219</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l7gaavpyrzgszhjhgkw45xnffa">fatcat:l7gaavpyrzgszhjhgkw45xnffa</a> </span>
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Detection of Functionally Important Regions in "Hypothetical Proteins" of Known Structure

Guy Nimrod, Maya Schushan, David M. Steinberg, Nir Ben-Tal
<span title="">2008</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
A web-server implementation of PatchFinder and the N-Func database are available at http://patchfinder.tau.ac.il/.  ...  To this end, we used (an improved version of) the PatchFinder algorithm for the detection of functional regions on the protein surface, which could mediate its interactions with, e.g., substrates, ligands  ...  We would like to acknowledge Leonid Brodsky, Sarel Fleishman, Yanay Ofran, Gilad Wainreb, Lei Xie, and Tsaffrir Zor for helpful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2008.10.017">doi:10.1016/j.str.2008.10.017</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19081051">pmid:19081051</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vhpi4i4v6vapjh2sob4r5mkbxu">fatcat:vhpi4i4v6vapjh2sob4r5mkbxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20131005173318/http://safrabio.cs.tau.ac.il/download/Papers/Guy_Nimrod_et_al_2008.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b8/2d/b82dd4c302692cccd5128a9bec80f636d8df3716.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2008.10.017"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Adaptively-Branching Fuzzy Greedy K-mean Decision Forest (FGK-DF) Model for Protein Local Tertiary Structure Prediction

Bernard Chen, Cody Hudson, Aaron Crawford, Minwoo Kim, Dongsheng Che
<span title="">2014</span> <i title="Columbia International Publishing"> American Journal of Bioinformatics and Computational Biology </i> &nbsp;
This work propose the Adaptively-Branching Fuzzy Greedy K-means-Decision Forest (FGK-DF) model, which utilizes conserved sequential and structural motifs that transcend protein family boundaries, to predict  ...  As such, in order to develop the dataset used for training and validation of the model, the Protein Sequence Culling Server (PISCES) based on Wang and Dunbrack (2003) , Homology derived Secondary Structure  ...  Like most approaches, the FGK-DF model does not interface with the PDB directly, but makes use of several additional servers and databases to filter, cull, and expand the information provided by the PDB  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7726/ajbcb.2014.1001">doi:10.7726/ajbcb.2014.1001</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ijasnzzupfdm5p3u4nk4jst6ry">fatcat:ijasnzzupfdm5p3u4nk4jst6ry</a> </span>
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