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Blind prediction of HIV integrase binding from the SAMPL4 challenge

David L. Mobley, Shuai Liu, Nathan M. Lim, Karisa L. Wymer, Alexander L. Perryman, Stefano Forli, Nanjie Deng, Justin Su, Kim Branson, Arthur J. Olson
<span title="2014-03-05">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqrkonq3ofesljyzeksgdlfeb4" style="color: black;">Journal of Computer-Aided Molecular Design</a> </i> &nbsp;
NIH Public Access Abstract Here, we give an overview of the protein-ligand binding portion of the SAMPL4 challenge, which focused on predicting binding of HIV integrase inhibitors in the catalytic core  ...  Pose prediction was also quite challenging, in part because inhibitors in the set bind to three different sites, so even identifying the correct binding site was challenging.  ...  We are also thankful to Tom Peat (CSIRO) and colleagues for the experimental data which made the integrase portion of SAMPL possible, and helped initiate SAMPL4.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10822-014-9723-5">doi:10.1007/s10822-014-9723-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24595873">pmid:24595873</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4331050/">pmcid:PMC4331050</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h22en4cr7fdpll7d3cuyaflcve">fatcat:h22en4cr7fdpll7d3cuyaflcve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308030528/http://pdfs.semanticscholar.org/ebbc/314e5da3aee4ced7053ad00ecb7a2570e1e8.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/eb/bc/ebbc314e5da3aee4ced7053ad00ecb7a2570e1e8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10822-014-9723-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331050" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Virtual screening of the SAMPL4 blinded HIV integrase inhibitors dataset

Claire Colas, Bogdan I. Iorga
<span title="2014-01-24">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqrkonq3ofesljyzeksgdlfeb4" style="color: black;">Journal of Computer-Aided Molecular Design</a> </i> &nbsp;
Several combinations of docking software and scoring functions were evaluated for their ability to predict the binding of a dataset of potential HIV integrase inhibitors.  ...  These protocols could successfully predict respectively 20.0% and 23.6% of the HIV integrase binders, all of them being present in the LEDGF site.  ...  Mobley, for providing the experimental data required for the evaluation of our predictions, as well as for the alternate analysis of the virtual screening results.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10822-014-9707-5">doi:10.1007/s10822-014-9707-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24458507">pmid:24458507</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lakva3sdnvevfc3u3szrm25hb4">fatcat:lakva3sdnvevfc3u3szrm25hb4</a> </span>
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Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge

Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins, Arthur J. Olson
<span title="2014-02-04">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqrkonq3ofesljyzeksgdlfeb4" style="color: black;">Journal of Computer-Aided Molecular Design</a> </i> &nbsp;
This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site)  ...  on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge.  ...  Emilio Gallicchio for their collaboration on the SAMPL4 Challenge using their BEDAM software.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10822-014-9709-3">doi:10.1007/s10822-014-9709-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24493410">pmid:24493410</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4053500/">pmcid:PMC4053500</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a3fnihbabrdjpip7bl4tzactmu">fatcat:a3fnihbabrdjpip7bl4tzactmu</a> </span>
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Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

Emilio Gallicchio, Nanjie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, Ronald M. Levy
<span title="2014-02-07">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqrkonq3ofesljyzeksgdlfeb4" style="color: black;">Journal of Computer-Aided Molecular Design</a> </i> &nbsp;
As part of the SAMPL4 blind challenge, filtered AutoDock Vina ligand docking predictions and large scale binding energy distribution analysis method binding free energy calculations have been applied to  ...  the virtual screening of a focused library of candidate binders to the LEDGF site of the HIV integrase protein.  ...  Acknowledgments This work has been supported in part by Research Grants from the National Institute of Health (GM30580 and P50 GM103368).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10822-014-9711-9">doi:10.1007/s10822-014-9711-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24504704">pmid:24504704</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4137862/">pmcid:PMC4137862</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/auspnc4zuras7deaaor5rnfghq">fatcat:auspnc4zuras7deaaor5rnfghq</a> </span>
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BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge

Emilio Gallicchio, Haoyuan Chen, He Chen, Michael Fitzgerald, Yang Gao, Peng He, Malathi Kalyanikar, Chuan Kao, Beidi Lu, Yijie Niu, Manasi Pethe, Jie Zhu (+1 others)
<span title="2015-03-01">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqrkonq3ofesljyzeksgdlfeb4" style="color: black;">Journal of Computer-Aided Molecular Design</a> </i> &nbsp;
The Binding Energy Distribution Analysis Method (BEDAM) protocol has been employed as part of the SAMPL4 blind challenge to predict the binding free energies of a set of octa-acid host-guest complexes.  ...  The resulting predictions were consistently judged as some of the most accurate predictions in this category of the SAMPL4 challenge in terms of quantitative accuracy and statistical correlation relative  ...  Acknowledgments This work has been supported in part by research grants from the National Institute of Health (GM30580) and the National Science Foundation Cyber-enabled Discovery and Innovation Award  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10822-014-9795-2">doi:10.1007/s10822-014-9795-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25726024">pmid:25726024</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4832917/">pmcid:PMC4832917</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rznfuqii25eoxhupazr7xtd3uu">fatcat:rznfuqii25eoxhupazr7xtd3uu</a> </span>
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Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

Nanjie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mentes, Emilio Gallicchio, Ronald M. Levy
<span title="2016-08-25">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqrkonq3ofesljyzeksgdlfeb4" style="color: black;">Journal of Computer-Aided Molecular Design</a> </i> &nbsp;
We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90.  ...  Prime MM-GBSA for the Hsp90 data set in this blind challenge.  ...  that were studied in the SAMPL4 HIV Integrase challenge, and for predicting the binding pose prior to the higher resolution FEP calculations of binding affinity.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10822-016-9952-x">doi:10.1007/s10822-016-9952-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27562018">pmid:27562018</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5869689/">pmcid:PMC5869689</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/flkyagqv5fgzlezomzplgntdb4">fatcat:flkyagqv5fgzlezomzplgntdb4</a> </span>
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Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation

Ahmet Mentes, Nan-Jie Deng, R. S. K. Vijayan, Junchao Xia, Emilio Gallicchio, Ronald M. Levy
<span title="2016-04-26">2016</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/z2ruvhjfujanbnydakuxtjslca" style="color: black;">Journal of Chemical Theory and Computation</a> </i> &nbsp;
The method is tested on a standard benchmark (T4 Lysozyme/ L99A/p-xylene complex) and on a library of HIV-1 integrase complexes derived from the SAMPL4 blind challenge.  ...  HIV-1 Integrase/ Ligands from SAMPL4 study-Previously, as part of the HIV-1 integrase virtual screening SAMPL4 challenge, 35,36 over 300 ligands were studied to screen Mentes et al.  ...  We also thank Peng He for giving the initial structures of HIV Integrase protein and full set of ligands from the SAMPL4 study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jctc.6b00134">doi:10.1021/acs.jctc.6b00134</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27070865">pmid:27070865</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4862910/">pmcid:PMC4862910</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t2ehb2ei2jev3jcbwpojpz4xk4">fatcat:t2ehb2ei2jev3jcbwpojpz4xk4</a> </span>
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Parameterization of an effective potential for protein-ligand binding from host-guest affinity data

Lauren Wickstrom, Nanjie Deng, Peng He, Ahmet Mentes, Crystal Nguyen, Michael K. Gilson, Tom Kurtzman, Emilio Gallicchio, Ronald M. Levy
<span title="2015-08-10">2015</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lml5dbm4jnfmjitqk6yu3nrfd4" style="color: black;">Journal of Molecular Recognition</a> </i> &nbsp;
These new solvation parameters were used to study protein-ligand binding in two drug targets against the HIV-1 virus and improved the agreement between the calculated and the experimental binding affinities  ...  Convergence of binding free energy calculations on CD host-guest systems can also be obtained rapidly, thus offering the opportunity to assess the robustness of these parameters.  ...  G. is a cofounder and has equity interest in the company VeraChem LLC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jmr.2489">doi:10.1002/jmr.2489</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26256816">pmid:26256816</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4715590/">pmcid:PMC4715590</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cc4qsmoabfhkpa4vofbkqpenfa">fatcat:cc4qsmoabfhkpa4vofbkqpenfa</a> </span>
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Computational Challenges of Structure-Based Approaches Applied to HIV [chapter]

Stefano Forli, Arthur J. Olson
<span title="">2015</span> <i title="Springer International Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/g7reubrhrneqxh5657kgb5whnm" style="color: black;">Current Topics in Microbiology and Immunology</a> </i> &nbsp;
Acknowledgments We thank IBM World Community Grid for the computational resource support provided to the FightAIDS@Home project. This work was supported by NIH R01 GM073087 and P50 GM103368 to AJO.  ...  The goal of the SAMPL4 challenge was a blind prediction of the binding of inhibitors into IN catalytic core domain (CCD).  ...  , and integrase.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/82_2015_432">doi:10.1007/82_2015_432</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25711462">pmid:25711462</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6yiwypppbbgt5jrojt4a2k44dq">fatcat:6yiwypppbbgt5jrojt4a2k44dq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190307174418/http://pdfs.semanticscholar.org/e43d/8507eb14b2881feddcc7d466d408124f7c26.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/e4/3d/e43d8507eb14b2881feddcc7d466d408124f7c26.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/82_2015_432"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Advancing Predictive Modeling Through Focused Development Of Model Systems To Drive New Modeling Innovations

David L. Mobley, John D. Chodera, Lyle Isaacs, Bruce C. Gibb
<span title="2016-10-05">2016</span> <i title="Zenodo"> Zenodo </i> &nbsp;
In recent years, blind prediction challenges have played a key role in driving innovations in prediction of physical properties and binding, especially in the form of the SAMPL series of challenges.  ...  This work seeks to advance quantitative methods for biomolecular design, especially for predicting biomolecular interactions, via a focused series of community blind prediction challenges.  ...  binding of fragments to trypsin and HIV integrase).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.163963">doi:10.5281/zenodo.163963</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/25w76ew3nvd2df7rmznzycdycq">fatcat:25w76ew3nvd2df7rmznzycdycq</a> </span>
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Asynchronous replica exchange software for grid and heterogeneous computing

Emilio Gallicchio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes, Ronald M. Levy
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wfenstutwram7ghf2w6rgf5gyu" style="color: black;">Computer Physics Communications</a> </i> &nbsp;
It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas.  ...  Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the  ...  E.G. and S.S. acknowledge support from the National Science Foundation (SI2-SSE 1440665). B.Z. acknowledges support from the Brooklyn College Research Foundation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cpc.2015.06.010">doi:10.1016/j.cpc.2015.06.010</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27103749">pmid:27103749</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4834714/">pmcid:PMC4834714</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7nmcgpw73fezxebow5zmaqbhta">fatcat:7nmcgpw73fezxebow5zmaqbhta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722110258/https://manuscript.elsevier.com/S0010465515002556/pdf/S0010465515002556.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/1d/68/1d68c3f885d25996d402d8b02842cd128041a57d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cpc.2015.06.010"> <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/PMC4834714" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Predicting binding free energies: Frontiers and benchmarks [article]

David L. Mobley, Michael K. Gilson
<span title="2016-09-11">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Simulations of the system are then used to compute thermodynamic information, such as binding affinities.  ...  Binding free energy calculations based on molecular simulations provide predicted affinities for biomolecular complexes.  ...  Indeed, blind predictions for a set of fragments binding to several sites formed part of the basis of the SAMPL4 challenge [122, 139] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/074625">doi:10.1101/074625</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/stasom7sbvhu3eqeeo7lalfubi">fatcat:stasom7sbvhu3eqeeo7lalfubi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503215332/https://www.biorxiv.org/content/biorxiv/early/2016/12/08/074625.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/b1/aa/b1aab384ec2392c9dc8b4fdae37ac07d5eb264a7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/074625"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

Majda Misini Ignjatović, Octav Caldararu, Geng Dong, Camila Muñoz-Gutierrez, Francisco Adasme-Carreño, Ulf Ryde
<span title="2016-08-26">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqrkonq3ofesljyzeksgdlfeb4" style="color: black;">Journal of Computer-Aided Molecular Design</a> </i> &nbsp;
of the predictions from the various methods.  ...  We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition.  ...  For the HIV integrase binding-affinity challenge in SAMPL4, a SIE approach was pointed out as best with a mean absolute deviation (MAD) of 5 kJ/mol, but it gave a negative correlation (R = -0.3) [20,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10822-016-9942-z">doi:10.1007/s10822-016-9942-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27565797">pmid:27565797</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5078160/">pmcid:PMC5078160</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5zhysvqf4vesvemorjrsyw4gti">fatcat:5zhysvqf4vesvemorjrsyw4gti</a> </span>
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Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

Samuel C. Gill, Nathan M. Lim, Patrick B. Grinaway, Ariën S. Rustenburg, Josh Fass, Gregory A. Ross, John D. Chodera, David L. Mobley
<span title="2018-02-27">2018</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;
Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges.  ...  Here, we focus on solving the binding mode prediction problem for rigid fragments.  ...  Acknowledgments DLM and SCG appreciate the financial support from the National Science Foundation (CHE 1352608) and the National Institutes of Health (1R01GM108889-01) and computing support from the UCI  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jpcb.7b11820">doi:10.1021/acs.jpcb.7b11820</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29486559">pmid:29486559</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5980761/">pmcid:PMC5980761</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4bvgfmafyngk7lyzolgxgxpdve">fatcat:4bvgfmafyngk7lyzolgxgxpdve</a> </span>
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FREE ENERGY SIMULATIONS AND STRUCTURAL STUDIES OF PROTEIN-LIGAND BINDING AND ALLOSTERY [article]

(:Unkn) Unknown, University, My, Ronald M. Levy, Vincent Voelz
<span title="2020-10-26">2020</span>
On the one hand, structural classification and feature identification of the structures of protein kinases, HIV proteins, and other extensively studied proteins would have an increasingly important role  ...  On the other hand, free energy calculations which include the conformational and binding free energy calculation, which provides the thermodynamics basis of protein allostery and inhibitor binding, have  ...  TG-MCB100145, and on the Garibaldi cluster at the Scripps Research Institute. We thank David Mobley and the SAMPL4 organizers.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.34944/dspace/1390">doi:10.34944/dspace/1390</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/smjq5bgjrjdyhf3qfyvg73zsqu">fatcat:smjq5bgjrjdyhf3qfyvg73zsqu</a> </span>
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