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The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite

Jared Adolf-Bryfogle, Roland L. Dunbrack Jr., Heinrich Sticht
<span title="2013-07-09">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;
Citation: Adolf-Bryfogle J, Dunbrack RL Jr (2013) The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite. PLoS ONE 8(7): e66856.  ...  General Rosetta options, such as -dun10 (the 2010 Dunbrack rotamer library [13] ) or -ex2 (extra chi2 rotamers), can be set through a window where a user can select from a few common options, enter custom  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0066856">doi:10.1371/journal.pone.0066856</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23874400">pmid:23874400</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3706480/">pmcid:PMC3706480</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kf47gph5rfeh3c2jrxp5cfmi2q">fatcat:kf47gph5rfeh3c2jrxp5cfmi2q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171007123138/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0066856&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/5e/05/5e054a472ab8768bcd4fc70748fb3b8d144f9972.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0066856"> <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/PMC3706480" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Proportionality: A Valid Alternative to Correlation for Relative Data

David Lovell, Vera Pawlowsky-Glahn, Juan José Egozcue, Samuel Marguerat, Jürg Bähler, Roland L. Dunbrack Jr.
<span title="2015-03-16">2015</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
In the life sciences, many measurement methods yield only the relative abundances of different components in a sample. With such relative-or compositional-data, differential expression needs careful interpretation, and correlation-a statistical workhorse for analyzing pairwise relationships-is an inappropriate measure of association. Using yeast gene expression data we show how correlation can be misleading and present proportionality as a valid alternative for relative data. We show how the
more &raquo; ... ength of proportionality between two variables can be meaningfully and interpretably described by a new statistic φ which can be used instead of correlation as the basis of familiar analyses and visualization methods, including co-expression networks and clustered heatmaps. While the main aim of this study is to present proportionality as a means to analyse relative data, it also raises intriguing questions about the molecular mechanisms underlying the proportional regulation of a range of yeast genes. Author Summary Relative abundance data is common in the life sciences; but appreciation that it needs special analysis and interpretation is scarce. Correlation is a popular as a statistical measure of pairwise association but should not be used on data that carry only relative information. Using timecourse yeast gene expression data, we show how correlation of relative abundances can lead to conclusions opposite to those drawn from absolute abundances, and that its value changes when different components are included in the analysis.Once all absolute information has been removed, only a subset of those associations will reliably endure in the remaining relative data, specifically, associations where pairs of values behave proportionally across observations. We propose a new statistic φ to describe the strength of proportionality between two variables and demonstrate how it can be straightforwardly used instead of correlation as the basis of familiar analyses and visualization methods.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1004075">doi:10.1371/journal.pcbi.1004075</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25775355">pmid:25775355</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4361748/">pmcid:PMC4361748</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5aytndximbcixn33eezxrm4yse">fatcat:5aytndximbcixn33eezxrm4yse</a> </span>
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Large-scale comparison of protein sequence alignment algorithms with structure alignments

J. Michael Sauder, Jonathan W. Arthur, Roland L. Dunbrack Jr.
<span title="2000-07-01">2000</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fkowqlvuffe5lnyfwblj3fcp7i" style="color: black;">Proteins: Structure, Function, and Bioinformatics</a> </i> &nbsp;
DALI has only recently become available (L. Holm, personal communication).  ...  We have a database available correlating the SEQRES and ATOM numbering (http://www.fccc.edu/research/labs/dunbrack/s2c).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/(sici)1097-0134(20000701)40:1&lt;6::aid-prot30&gt;3.0.co;2-7">doi:10.1002/(sici)1097-0134(20000701)40:1&lt;6::aid-prot30&gt;3.0.co;2-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10813826">pmid:10813826</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7yc5ega4sfg7nenhnhttktz5fq">fatcat:7yc5ega4sfg7nenhnhttktz5fq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20031029130317/http://www.bii.a-star.edu.sg:80/~atif/doc/Alignment/sauder00largescale.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/06/b5/06b5ef26e102c231206b68268dca814765676561.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/(sici)1097-0134(20000701)40:1&lt;6::aid-prot30&gt;3.0.co;2-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Development of a Rotamer Library for Use in β-Peptide Foldamer Computational Design

Scott J. Shandler, Maxim V. Shapovalov, Roland L. Dunbrack, Jr., William F. DeGrado
<span title="2010-06-02">2010</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/czzozsmlgreapacsfn45462e54" style="color: black;">Journal of the American Chemical Society</a> </i> &nbsp;
Dunbrack and M.  ...  Side chains were placed at the C 3 position of the central residue on each scaffold to create an L-β-amino acid.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ja906700x">doi:10.1021/ja906700x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20446685">pmid:20446685</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3079439/">pmcid:PMC3079439</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zm4wsn3y3jdkpmdjz5hmomms7a">fatcat:zm4wsn3y3jdkpmdjz5hmomms7a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208080330/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3079439&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/f2/b4/f2b47f2f635f406935608887ed6e19aad841bc44.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ja906700x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079439" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Understanding the physical basis for the side-chain conformational preferences of methionine

Alejandro Virrueta, Corey S. O'Hern, Lynne Regan
<span title="2016-04-06">2016</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fkowqlvuffe5lnyfwblj3fcp7i" style="color: black;">Proteins: Structure, Function, and Bioinformatics</a> </i> &nbsp;
Roland L. Dunbrack, Jr. for stimulating discussions.  ...  Stereochemistry of Met, Mse, and Nle dipeptide mimetics We studied hard-sphere, explicit hydrogen representations of Met (N-acetyl-L-Met-N'-methylamide), Nle (N-acetyl-L-Nle-N'-methylamide), and Mse (N-acetyl-L-Mse-N  ...  1.0 Å' and 'Dunbrack 1.7 Å' databases 25-27 for our calculations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.25026">doi:10.1002/prot.25026</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26917446">pmid:26917446</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hbft75vk2fgednj5xtt24zzne4">fatcat:hbft75vk2fgednj5xtt24zzne4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200322215341/https://jamming.research.yale.edu/files/papers/Virrueta.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/2e/0a/2e0aa6fb5433f56aadd3b405a20d05130fccaf24.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.25026"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Page 313 of Florida Bar Journal Vol. 68, Issue 8 [page]

<span title="">1994</span> <i title="Florida Bar Journal"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_florida-bar-journal" style="color: black;">Florida Bar Journal</a> </i> &nbsp;
. . . 78 DUKE,DavisWelby,Jr . .92 DUKE, Thomas Howard . .77 DUNBRACK.  ...  Wynne M, Jr . . 94 CASTILLO, Richard Paul . . .87 CASTLES, Donald Earl . . .94 CATALDO, Roland Nicholas . . 93 CATREN, Carolyn Kay . .91 CATRI, Wesley L . .92 CAULKINS, Charles S . 88 CAVANAGH, Brian Thomas  ... 
<span class="external-identifiers"> </span>
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ACKNOWLEDGMENTS [chapter]

<span title="2019-12-31">2019</span> <i title="University of California Press"> At Home in Nature </i> &nbsp;
Special thanks go to Kym Boyman and Beth Robinson, Chris Bensley Drain, Roland Dunbrack Jr., Janet M.  ...  I would not have become a scholar of religion, beginning in my undergraduate years, had it not been for my brilliant introduction to the field by Diana L.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1525/9780520937864-003">doi:10.1525/9780520937864-003</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yne7umyqljd4dlbzfmtm6nk6oi">fatcat:yne7umyqljd4dlbzfmtm6nk6oi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201107192407/https://www.degruyter.com/california/downloadpdf/book/9780520937864/10.1525/9780520937864-003.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/b4/cb/b4cbe3e480b7c6a58656da8a228b0451785d7e2d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1525/9780520937864-003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

Maxim V. Shapovalov, Roland L. Dunbrack
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
fashion in accordance with the one-dimensional c i backbone-independent density: l i = 0 B B B @ Q Nr j = 1 b f c À c j jrÀn Á 1 N r b f c ðc i jr Àn Þ 1 C C C A a = g 1d r b f c ðc i jr Àn Þ a ; (16)  ...  , 2002; Dunbrack and Cohen, 1997) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2011.03.019">doi:10.1016/j.str.2011.03.019</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21645855">pmid:21645855</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3118414/">pmcid:PMC3118414</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/domjwhixfbhgrh64ufcyhcs42a">fatcat:domjwhixfbhgrh64ufcyhcs42a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171002130006/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/b79/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDk2OTIxMjYxMTAwMTQ0NA%3D%3D.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/65/e9/65e9349b06447612ef0bb56ffd9049d080958b2c.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.2011.03.019"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118414" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction

Maxim Shapovalov, Roland L. Dunbrack, Slobodan Vucetic, Björn Wallner
<span title="2020-05-06">2020</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;
Project administration: Roland L. Dunbrack, Jr., Slobodan Vucetic. Resources: Roland L. Dunbrack, Jr. Software: Maxim Shapovalov. Supervision: Roland L. Dunbrack, Jr., Slobodan Vucetic.  ...  Funding acquisition: Roland L. Dunbrack, Jr. Investigation: Maxim Shapovalov, Roland L. Dunbrack, Jr., Slobodan Vucetic. Methodology: Maxim Shapovalov, Roland L. Dunbrack, Jr., Slobodan Vucetic.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0232528">doi:10.1371/journal.pone.0232528</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32374785">pmid:32374785</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/swmzjx4wivc4fbqmdczjmknlca">fatcat:swmzjx4wivc4fbqmdczjmknlca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200508065004/https://journals.plos.org/plosone/article/file?id=10.1371%2Fjournal.pone.0232528&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/09/e7/09e74ff73572aad4e2dedccc6104d3dc40d40e3a.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.0232528"> <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 new clustering and nomenclature for beta turns derived from high-resolution protein structures

Maxim Shapovalov, Slobodan Vucetic, Roland L. Dunbrack, Charlotte M. Deane
<span title="2019-03-07">2019</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Data curation: Maxim Shapovalov.Formal analysis: Maxim Shapovalov, Roland L. Dunbrack, Jr. Funding acquisition: Roland L. Dunbrack, Jr. Investigation: Maxim Shapovalov, Roland L. Dunbrack, Jr.  ...  Methodology: Maxim Shapovalov, Slobodan Vucetic, Roland L. Dunbrack, Jr. Software: Maxim Shapovalov. Supervision: Slobodan Vucetic, Roland L. Dunbrack, Jr. Validation: Maxim Shapovalov.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1006844">doi:10.1371/journal.pcbi.1006844</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30845191">pmid:30845191</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6424458/">pmcid:PMC6424458</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ynptebr7yrfppnikmyf22eovqy">fatcat:ynptebr7yrfppnikmyf22eovqy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501152459/https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006844&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/db/1e/db1e3854d979ed90901f5f08752176313f9c6210.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1006844"> <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/PMC6424458" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cyclic coordinate descent: A robotics algorithm for protein loop closure

Adrian A. Canutescu, Roland L. Dunbrack
<span title="">2003</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
Jr.  ...  Ramachandran probability maps We derived Ramachandran probabilities from data used to build our backbone-dependent rotamer libraries (May 2002 release; Dunbrack Jr. and Cohen 1997).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1110/ps.0242703">doi:10.1110/ps.0242703</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12717019">pmid:12717019</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2323867/">pmcid:PMC2323867</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/saunpvt6avfsjh4xf2yzf3ofzi">fatcat:saunpvt6avfsjh4xf2yzf3ofzi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809025618/https://www.ti.inf.ethz.ch/ew/courses/GCMB07/material/lecture06/canutescudunbrack-ccd-ps03.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/84/43/84430928c92e52fb9f8d2f8b1dd26000d5169387.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1110/ps.0242703"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323867" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations

David Punihaole, Zhenmin Hong, Ryan S. Jakubek, Elizabeth M. Dahlburg, Steven Geib, Sanford A. Asher
<span title="2015-09-30">2015</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ah52wn6qqbeilcx7mb5h3ozbeu" style="color: black;">Journal of Physical Chemistry B</a> </i> &nbsp;
Roland Dunbrack, Jr., for providing his rotamer database.  ...  L-seryl-L-asparagine (Ser-Asn, ≥99% purity) was purchased from Bachem.  ...  Plots showing Ramachandran angles for PDB entries from the Shapovalov and Dunbrack database of (a) Gln and (b) Asn.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jpcb.5b07651">doi:10.1021/acs.jpcb.5b07651</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26392216">pmid:26392216</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5065012/">pmcid:PMC5065012</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y5gwjwzrtzfxdjwxylpuit4djm">fatcat:y5gwjwzrtzfxdjwxylpuit4djm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209165338/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5065012&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/1c/a4/1ca40a461721d7c3c7ebfbd83e53b57bbc95e309.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jpcb.5b07651"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065012" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Meeting review: the Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13–16, 1996

Roland L Dunbrack, Dietlind L Gerloff, Michael Bower, Xiaowu Chen, Olivier Lichtarge, Fred E Cohen
<span title="">1997</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/i7qhweomhjfebdw6hgy7lr5wly" style="color: black;">Folding &amp; design</a> </i> &nbsp;
RL Dunbrack is an NIH Post-doctoral Fellow. DL Gerloff is a fellow of the Leukemia Society of America. O Lichtarge is an American Heart Association fellow.  ...  Review Meeting review: CASP2 Dunbrack et al. R29 Review Meeting review: CASP2 Dunbrack et al. R35  ...  Rychlewski, B Zhang, L Jaroszewski, K Pawlowski, B Reva (Scripps Institute) U HOBOHM (Roche, Basel) B HONIG, A Yang, L Xiao (Columbia University) T HUBBARD, JH Park, A Reinhardt (University of Cambridge  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1359-0278(97)00011-4">doi:10.1016/s1359-0278(97)00011-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9135979">pmid:9135979</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c6yh4fsnrbblfk45htixf7px4i">fatcat:c6yh4fsnrbblfk45htixf7px4i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190313171914/https://core.ac.uk/download/pdf/82029613.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/48/04/48045f72960b00fa4eee74a87b9c9bbe4d286d56.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1359-0278(97)00011-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4

Qifang Xu, Qingling Tang, Panagiotis Katsonis, Olivier Lichtarge, David Jones, Samuele Bovo, Giulia Babbi, Pier L. Martelli, Rita Casadio, Gyu Rie Lee, Chaok Seok, Aron W. Fenton (+1 others)
<span title="2017-05-02">2017</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2vzjuzyygveinhd4ab2ux34qv4" style="color: black;">Human Mutation</a> </i> &nbsp;
In most binary phenotype prediction assessments (Wei and Dunbrack Jr, 2013) , it is important to balance the success of positive predictions and/or experimental outcomes with negative predictions and/  ...  The structure was assembled by superposing monomers from several structures of homologues of L-PYK with PEP, ADP, and alanine bound onto a tetrameric structure of human L-PYK with fructose-1,6bisphosphate  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/humu.23222">doi:10.1002/humu.23222</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28370845">pmid:28370845</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/etpifi25bzbjjgchq3p4a6bznq">fatcat:etpifi25bzbjjgchq3p4a6bznq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724063149/http://discovery.ucl.ac.uk/1547713/1/humu23222.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/6b/6a/6b6a73cc4473c5c1be53d2c9341b554ac93f6c65.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/humu.23222"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences

Bulat Faezov, Roland L. Dunbrack, Yang Zhang
<span title="2021-07-06">2021</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;
Author Contributions Conceptualization: Roland L. Dunbrack, Jr. Data curation: Bulat Faezov.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0253411">doi:10.1371/journal.pone.0253411</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34228733">pmid:34228733</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8259974/">pmcid:PMC8259974</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pad7pxs6xjbgzgzlobm54anhu4">fatcat:pad7pxs6xjbgzgzlobm54anhu4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210720032944/https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pone.0253411/1/pone.0253411.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&amp;X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210720%2Fauto%2Fstorage%2Fgoog4_request&amp;X-Goog-Date=20210720T032942Z&amp;X-Goog-Expires=86400&amp;X-Goog-SignedHeaders=host&amp;X-Goog-Signature=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" 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/a6/09/a60963f56af80acf126b6dcfcee398dd9c426466.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0253411"> <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/PMC8259974" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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