Filters








15,220 Hits in 3.1 sec

Protein flexibility in docking and surface mapping

Katrina W. Lexa, Heather A. Carlson
<span title="2012-05-09">2012</span> <i title="Cambridge University Press (CUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jns6cvwyffcm3ojmxntl7de3mu" style="color: black;">Quarterly Reviews of Biophysics (print)</a> </i> &nbsp;
Typical protein-ligand docking efforts still rely on a single rigid receptor, which is an incomplete representation of potential binding conformations of the protein.  ...  This review examines the current toolbox for flexible protein-ligand docking and receptor surface mapping. Present limitations and possibilities for future development are discussed.  ...  Acknowledgments This work has been supported by the National Institutes of Health (GM65372).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s0033583512000066">doi:10.1017/s0033583512000066</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22569329">pmid:22569329</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4272345/">pmcid:PMC4272345</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s7voxcdb7zbyrgkt7kedvo3lky">fatcat:s7voxcdb7zbyrgkt7kedvo3lky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200502093948/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4272345&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/78/d8/78d8edc80cef84dc29a53d90ca426d41759ee30a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s0033583512000066"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> cambridge.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272345" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Flexible ligand docking to multiple receptor conformations: a practical alternative

Maxim Totrov, Ruben Abagyan
<span title="">2008</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uzv6ve6frfevrcjkqzfvw36bfu" style="color: black;">Current Opinion in Structural Biology</a> </i> &nbsp;
Acknowledgements The authors thank Irina Kufareva and Giovanni Bottegoni for helpful discussions and artistic assistance, and Kim Reynolds for reviewing the manuscript.  ...  The original DOCK algorithm was also extended to ensembles of receptor structures, and a comparative study of the MRC docking versus the 'soft' docking potential was reported by Ferrari et al.  ...  The antagonist bound androgen receptor models were generated using a ligand-steered pocket generator and an ensemble docking of the benchmark ligands. of the marketed drugs for potential androgen receptor  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.sbi.2008.01.004">doi:10.1016/j.sbi.2008.01.004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18302984">pmid:18302984</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2396190/">pmcid:PMC2396190</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rfcim5chdvhozf3s5jxfwydsmy">fatcat:rfcim5chdvhozf3s5jxfwydsmy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809132045/http://www.cmbi.ru.nl/edu/bioinf4/articles/pdf/vsc_abagyan_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/24/90/2490169d931c9501adc03935bd9654c0ee541ae2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.sbi.2008.01.004"> <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/PMC2396190" 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 challenges of protein flexibility in drug design

Dinler A Antunes, Didier Devaurs, Lydia E Kavraki
<span title="2015-09-28">2015</span> <i title="Informa Healthcare"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4m2squtugrdvtgjdvfbz5jhmaq" style="color: black;">Expert Opinion on Drug Discovery</a> </i> &nbsp;
In this context, the combination of ensemble and selective docking can show limitations. First, no matter how good the conformational ensemble is, it is only a discrete collection of states.  ...  of protein flexibility. • VS can benefit from combining ensemble docking and selective docking. • GP is pushing the boundaries of molecular docking, focusing on complex systems and realistic binding predictions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1517/17460441.2015.1094458">doi:10.1517/17460441.2015.1094458</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26414598">pmid:26414598</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3cdp5prnkrdddd6sh5rita7yja">fatcat:3cdp5prnkrdddd6sh5rita7yja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226065946/http://pdfs.semanticscholar.org/6de2/4452d9130404671e630bec012446346e095b.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/6d/e2/6de24452d9130404671e630bec012446346e095b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1517/17460441.2015.1094458"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Induced fit docking, and the use of QM/MM methods in docking

Mengang Xu, Markus A. Lill
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6b7t23yr6ffophcymqusi2ilgm" style="color: black;">Drug Discovery Today : Technologies</a> </i> &nbsp;
Although widely used, the predictive reliability of docking methods is often limited by the inability to accurately and efficiently model protein flexibility and quantify binding strength.  ...  Docking methods are popular computational techniques in drug discovery to identify new active molecules that bind to a given biological target.  ...  Acknowledgments We thank Laura Kingsley for critical reading of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ddtec.2013.02.003">doi:10.1016/j.ddtec.2013.02.003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24050138">pmid:24050138</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3719877/">pmcid:PMC3719877</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mi7ovchymrgtddcbx464odzvvu">fatcat:mi7ovchymrgtddcbx464odzvvu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200207171403/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3719877&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/bd/7e/bd7ec91112d7a6effa2353d5246297a62830ccbd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ddtec.2013.02.003"> <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/PMC3719877" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

Giovanni Bottegoni, Irina Kufareva, Maxim Totrov, Ruben Abagyan
<span title="2009-01-22">2009</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/biqbvvfsgzd3tgqsg6hhdhdk2u" style="color: black;">Journal of Medicinal Chemistry</a> </i> &nbsp;
limited size and diversity.  ...  the accuracy of traditional ensemble docking.  ...  Supporting Information Available: Complete list of PDB structures employed in the study, the detailed results of the ligand docking simulations for each ensemble, the complete description of the cluster  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/jm8009958">doi:10.1021/jm8009958</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19090659">pmid:19090659</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2662720/">pmcid:PMC2662720</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oidq6mwlzbdgfmo2a7rwwm65tq">fatcat:oidq6mwlzbdgfmo2a7rwwm65tq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200320163524/http://www-ablab.ucsd.edu/pdf/09_4D_Bottegoni_JMC.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/82/1a/821a3f8e2192d5aa4824b5c889c93eb3b24a1847.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/jm8009958"> <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/PMC2662720" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Molecular docking to ensembles of protein structures 1 1Edited by B. Honig

Ronald M.A Knegtel, Irwin D Kuntz, C.M Oshiro
<span title="">1997</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
Both methods have been applied in docking small molecules to ensembles of crystal and solution structures, and we show that experimentally determined binding orientations and computed energies of known  ...  . # 1997 Academic Press Limited  ...  Limitations The use of ensembles of discrete conformations to mimic receptor¯exibility poses certain limitations on the accuracy and scope of the methodology described here.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1006/jmbi.1996.0776">doi:10.1006/jmbi.1996.0776</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9047373">pmid:9047373</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6lc7qiqnqze2rm4g2ge5ip4av4">fatcat:6lc7qiqnqze2rm4g2ge5ip4av4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810001335/https://users.cs.duke.edu/~brd/Teaching/Bio/asmb/current/Papers/Lit4Docking/ensembleDock.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/7f/2e/7f2e2db782c4cbcd25b141239a029b46563c2085.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1006/jmbi.1996.0776"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan
<span title="2010-01-25">2010</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uilc246nrbhffhjy3flluhazbi" style="color: black;">Journal of Chemical Information and Modeling</a> </i> &nbsp;
and, second, to find the properties of the best-performing conformers that can be used to select a smaller set of conformers for ensemble docking.  ...  Here we used a very large and diverse benchmark of 1068 X-ray protein conformations of 99 therapeutically relevant proteins, first, to compare the performance of the ensemble and single-conformation docking  ...  size of the space to be sampled and limited accuracy of the energy functions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ci9003943">doi:10.1021/ci9003943</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20000587">pmid:20000587</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2811216/">pmcid:PMC2811216</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/v7wliyjdfndixj7o5mozlihcwa">fatcat:v7wliyjdfndixj7o5mozlihcwa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120130204248/http://abagyan.ucsd.edu/pdf/10_Recipes_Rueda_JCIM.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/cf/2a/cf2aae52b7d7987a02c48fc2644654416cc3357e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ci9003943"> <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/PMC2811216" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Retrospective Ensemble Docking of Allosteric Modulators in an Adenosine G-Protein-Coupled Receptor [article]

Apurba Bhattarai, Jinan Wang, Yinglong Miao
<span title="2020-01-13">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Ensemble docking has proven useful in drug discovery and development.  ...  Results: Ensemble docking outperforms docking of the receptor cryo-EM structure.  ...  However, proteins have been often considered rigid, largely limiting the successful rate of docking.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.01.11.902809">doi:10.1101/2020.01.11.902809</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k7yz3gczvbaqfn77jghghry4eq">fatcat:k7yz3gczvbaqfn77jghghry4eq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200325100608/https://www.biorxiv.org/content/biorxiv/early/2020/01/13/2020.01.11.902809.full.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/fe/f5/fef57af07f441a514095621725d70afcbbadbdc2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.01.11.902809"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Ensemble-based docking: From hit discovery to metabolism and toxicity predictions

Wilfredo Evangelista, Rebecca L. Weir, Sally R. Ellingson, Jason B. Harris, Karan Kapoor, Jeremy C. Smith, Jerome Baudry
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/74assiiqmjamth6tcvry4hichm" style="color: black;">Bioorganic &amp; Medicinal Chemistry</a> </i> &nbsp;
This paper describes and illustrates the use of ensemble-based docking, i.e., using a collection of protein structures in docking calculations for hit discovery, the exploration of biochemical pathways  ...  We show examples where ensemble-based docking has significantly increased the number and the diversity of validated drug candidates.  ...  Biotechnology at the University of Tennessee for the PCB-30 estrogenization pathway project, and Shifa Biomedical and the laboratory of Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bmc.2016.07.064">doi:10.1016/j.bmc.2016.07.064</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27543390">pmid:27543390</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5073379/">pmcid:PMC5073379</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cbg6tg3wtrfyzglyznoh4pjxxm">fatcat:cbg6tg3wtrfyzglyznoh4pjxxm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211101024/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5073379&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/32/c1/32c1506718d866af6c4b3026fd21b239e504ad53.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bmc.2016.07.064"> <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/PMC5073379" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles

Sidhartha Chaudhury, Jeffrey J. Gray
<span title="">2008</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
Backbone flexibility was limited to the smaller partner of the complex, structural ensembles were generated using Rosetta refinement methods, and docking consisted of local perturbations around the complexed  ...  The marked success of CS and CS/IF docking shows that ensemble docking can be a versatile and effective method for accommodating conformational plasticity in docking and serves as a demonstration for the  ...  Acknowledgements We acknowledge Michael Daily, Monica Berrondo, Arvind Sivasubramanian, and Chu Wang for insightful discussions and for reading and editing of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2008.05.042">doi:10.1016/j.jmb.2008.05.042</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18640688">pmid:18640688</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2573042/">pmcid:PMC2573042</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kvns6zs3b5c75iaqlc4pdtqhay">fatcat:kvns6zs3b5c75iaqlc4pdtqhay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110331193252/http://graylab.jhu.edu/publications/2008JMB.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/64/ae/64ae9cbb9fe5511dfb146408eadb5d701eca80d7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2008.05.042"> <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/PMC2573042" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ensemble Docking in Drug Discovery

Rommie E. Amaro, Jerome Baudry, John Chodera, Özlem Demir, J. Andrew McCammon, Yinglong Miao, Jeremy C. Smith
<span title="">2018</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
This review gives a historical account of the development of ensemble docking and discusses some pertinent methodological advances in conformational sampling.  ...  Ensemble docking corresponds to the generation of an "ensemble" of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that  ...  converged ensembles of flexible target structures for use in ensemble docking.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2018.02.038">doi:10.1016/j.bpj.2018.02.038</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29606412">pmid:29606412</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6129458/">pmcid:PMC6129458</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6kyspe4scneenklkuotmzs7xhe">fatcat:6kyspe4scneenklkuotmzs7xhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210102534/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6129458&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/e9/1ce97791de11c7324c92f7a6c2678d45c5985eea.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2018.02.038"> <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/PMC6129458" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design

William Sinko, Steffen Lindert, J. Andrew McCammon
<span title="2012-12-17">2012</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rmbcp7jqnngqhoni4nr5jv76zq" style="color: black;">Chemical Biology and Drug Design</a> </i> &nbsp;
We investigate modifications to standard rigid receptor docking algorithms and also explore enhanced sampling techniques, and the combination of free energy calculations and enhanced sampling techniques  ...  These developments may help improve the efficiency of drug discovery and development.  ...  See Figure 2 for a schematic of ensemble-based docking methods.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/cbdd.12051">doi:10.1111/cbdd.12051</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23253130">pmid:23253130</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3540989/">pmcid:PMC3540989</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tso4kv2zqrfmndvfkekcw3f24a">fatcat:tso4kv2zqrfmndvfkekcw3f24a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809055808/http://users.mccammon.ucsd.edu/~slindert/papers/cbdd.12051.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/8f/fe/8ffe521b7627dcf07d5a90afbb4f670a7d8cb371.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/cbdd.12051"> <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/PMC3540989" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational binding study with α7 nicotinic acetylcholine receptor of Anvylic-3288: an allosteric modulator

Ankit Ganeshpurkar, Ravi Singh, Devendra Kumar, Divya, Shalini Shivhare, Ashok Kumar, Sushil Kumar Singh
<span title="2020-08-24">2020</span> <i title="Taylor &amp; Francis"> figshare.com </i> &nbsp;
Nicotinic receptors are ligand-gated ion channels, involved in the generation of action potential in post synaptic membrane and motor endplate.  ...  Docking study displayed that a1 binding modes had better binding energies than the t1 and v1 modes.  ...  Number of GA run Population size Maximum number of generations Maximum number of evaluations Rate of Gene mutation Rate of crossing over Molecular docking 500 150 27000 2500000  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.12849047.v1">doi:10.6084/m9.figshare.12849047.v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s3b4sxkmkfcj3oe6bs2zd3ckva">fatcat:s3b4sxkmkfcj3oe6bs2zd3ckva</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200825010154/https://s3-eu-west-1.amazonaws.com/pstorage-tf-iopjsd8797887/24407510/gmos_a_1795166_sm7964.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/c2/75/c27529cfaa53faf0427fbcff91020104570bbc6e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.12849047.v1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> figshare.com </button> </a>

ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease

Simon Leis, Martin Zacharias, Yaakov Koby Levy
<span title="2012-10-24">2012</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;
For the retroviral protease the method was tested on an ensemble of protease structures crystallized in the presence of different ligands and on a set of structures obtained from morphing between the unbound  ...  A new docking approach, ReFlexIn (Receptor Flexibility by Interpolation), that combines receptor flexibility with the computationally efficient potential grid representation of receptor molecules has been  ...  In contrast to other ensemble docking approaches the ReFlexIn method allows for a smooth and continuous deformation of the receptor structure along a series of snapshots by interpolation between potential  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0048008">doi:10.1371/journal.pone.0048008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23110159">pmid:23110159</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3480487/">pmcid:PMC3480487</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iinfkfwrp5hvhbiop6tc2nxrni">fatcat:iinfkfwrp5hvhbiop6tc2nxrni</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171005045951/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0048008&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/9e/a0/9ea0385cc29d651f5f3cb84b7b94f82ff8e79dfa.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.0048008"> <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/PMC3480487" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dancing Molecules: Rewiring Cooperative Communications within 14-3-3 ζ Docking Proteins [article]

Leroy Keith Davis
<span title="2019-06-27">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
And accentuated nonrandom patterns of deformation waves resulting in a gain of function mutation characterized by increased protein flexibility.  ...  Notably, synthetic evolution by FTEF anticipated evolution of the 14-3-3 zeta; docking protein.  ...  Acknowledgements This work used Extreme Science and Engineering Discovery Environment (XSEDE) that is supported by National Science Foundation grant ACI-1548562.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/683466">doi:10.1101/683466</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/imeqohx3arawzgujzh6tllcdlu">fatcat:imeqohx3arawzgujzh6tllcdlu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200323043935/https://www.biorxiv.org/content/biorxiv/early/2019/06/27/683466.full.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/ea/2c/ea2c6a23acf2ebf5e35742b4f8dd448274d433f7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/683466"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 15,220 results