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Solvated protein–DNA docking using HADDOCK

Marc van Dijk, Koen M. Visscher, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin
<span title="2013-04-30">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cimmcbrwkbf4xblwfxyaslsraa" style="color: black;">Journal of Biomolecular NMR</a> </i> &nbsp;
Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation.  ...  We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution  ...  This allows evaluating both the effect of explicit solvation on the quality of the docking models and the recovery of interfacial water molecules with respect to the reference complex.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10858-013-9734-x">doi:10.1007/s10858-013-9734-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23625455">pmid:23625455</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lt27onysiffj7h7kf4km2yhr5q">fatcat:lt27onysiffj7h7kf4km2yhr5q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200311010114/https://dspace.library.uu.nl/bitstream/handle/1874/290382/article_post-print.pdf;jsessionid=9EEF2A1A03721AEDEE5445B2E63630C8?sequence=3" 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/79/66/79667b95217350edaaacc8aba68059c96e8753a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10858-013-9734-x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Atomic solvation parameters in the analysis of protein-protein docking results

Maxwell D. Cummings, Randy J. Read, Trevor N. Hart
<span title="">1995</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
For most of the docking results we analyzed, the use of an octanol-water-based ASP set marginally improved the energetic ranking of the low-energy dockings, whereas the other ASP sets we tested disturbed  ...  the ranking of the low-energy dockings in many of the same systems.  ...  Acknowledgments One of the reviewers alerted us to the studies regarding water entrainment by solutes in partition systems, as well as the backbone study by Wolfenden's group.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.5560041014">doi:10.1002/pro.5560041014</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/8535245">pmid:8535245</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2142991/">pmcid:PMC2142991</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eo3lvuqetbc3zkpdimlkgvym6u">fatcat:eo3lvuqetbc3zkpdimlkgvym6u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208172439/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2142991&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/e4/10/e410d96f3049d155035901c30902158a430ff103.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.5560041014"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2142991" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CIRSE: A solvation energy estimator compatible with flexible protein docking and design applications

David S. Cerutti, Tushar Jain, J. Andrew McCammon
<span title="">2006</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
energies of designed sequences as well as putative docked complexes.  ...  We apply the model in energy minimization, rotamer optimization, protein design, and protein docking applications.  ...  This research was supported in part by grants from the NSF, the NIH, the Center for Theoretical Biological Physics, the National Biomedical Computation Resource, the San Diego Supercomputer Center, Accelrys  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1110/ps.051985106">doi:10.1110/ps.051985106</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16815913">pmid:16815913</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2242569/">pmcid:PMC2242569</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yfxujn7stbesnd6n3xjjwxhole">fatcat:yfxujn7stbesnd6n3xjjwxhole</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191128165258/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2242569&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/48/10/4810f2e1d5723ef6648ae90907e508c8e241da4b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1110/ps.051985106"> <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/PMC2242569" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

How 'Protein-Docking' Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids?

Francesca Tessaro, Leonardo Scapozza
<span title="2020-06-13">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dstyyzbt45gknhqqjsh45p55h4" style="color: black;">Molecules</a> </i> &nbsp;
In this review, we retraced the '40-year evolution' of molecular docking algorithms.  ...  Over the course of the years, their development allowed to progress from the so-called 'rigid-docking' searching methods to the more sophisticated 'semi-flexible' and 'flexible docking' algorithms.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/molecules25122749">doi:10.3390/molecules25122749</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32545835">pmid:32545835</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rhfd7634qzcuxpsnhmqpzityom">fatcat:rhfd7634qzcuxpsnhmqpzityom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200617010831/https://res.mdpi.com/d_attachment/molecules/molecules-25-02749/article_deploy/molecules-25-02749-v3.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/bb/78/bb782dd4b898310c23f670eab6675130fa8060cf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/molecules25122749"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Molecular theory of solvation: Methodology summary and illustrations

Kovalenko
<span title="">2015</span> <i title="Institute for Condensed Matter Physics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7korb2h5hnddfauld2xzgfzx3m" style="color: black;">Condensed Matter Physics</a> </i> &nbsp;
One of the versions of this formalism, the three-dimensional reference interaction site model (3D-RISM) integral equation complemented with the Kovalenko-Hirata (KH) closure approximation, yields the solvation  ...  Integral equation theory of molecular liquids based on statistical mechanics is quite promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution.  ...  Acknowledgements The work was supported by the National Institute for Nanotechnology, National  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5488/cmp.18.32601">doi:10.5488/cmp.18.32601</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zuw67sq465d77lpzduqgrj5onm">fatcat:zuw67sq465d77lpzduqgrj5onm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721182153/http://nparc.nrc-cnrc.gc.ca/eng/view/fulltext/?id=53020f23-1ac2-41af-8879-1819d3a6fe4f" 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/ca/c2/cac266b2196619c7fa6a409c6873c236b5dfa521.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5488/cmp.18.32601"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking [article]

Ryan E Pavlovicz, Hahnbeom Park, Frank DiMaio
<span title="2019-04-25">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We introduce an updated energy model that efficiently captures the energetic effects of these highly-coordinated water molecules on the surfaces of proteins.  ...  This "semi-explicit" water model is implemented in Rosetta and allows for simultaneous prediction of side chain conformation and coordinated water geometry; the approach is suitable for structure prediction  ...  Acknowledgements: This work was facilitated though the use of advanced computational, storage, and networking infrastructure provided by the Hyak supercomputer system at the University of Washington.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/618603">doi:10.1101/618603</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jfxl2xhb4rhshmzy22drwyi4dy">fatcat:jfxl2xhb4rhshmzy22drwyi4dy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324105512/https://www.biorxiv.org/content/biorxiv/early/2019/04/25/618603.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/81/48/814816c66134a1385f152f718ecd4fc79d1ef8aa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/618603"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Advances in the treatment of explicit water molecules in docking and binding free energy calculations

Xiao Hu, Irene Maffucci, Alessandro Contini
<span title="2018-05-14">2018</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wsglambh6jg5pc2gek5luzhfky" style="color: black;">Current Medicinal Chemistry</a> </i> &nbsp;
Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions.  ...  Results: Here, we analyse software to aid the selection, or to predict the position, of water molecules that are going to be explicitly considered in later docking studies.  ...  kinase inhibitor design, [75] and providing initial solvated model for MD simulations of ATP-bound Akt1 complex  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/0929867325666180514110824">doi:10.2174/0929867325666180514110824</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29756561">pmid:29756561</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bfozkucimrdlpi74dcbi2jx54y">fatcat:bfozkucimrdlpi74dcbi2jx54y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200306091640/https://air.unimi.it/retrieve/handle/2434/579643/1042164/Review_CMC_19-02-18_postprint.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/ad/d3/add37af1dc6e3463972791a28651018929bfeb09.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/0929867325666180514110824"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination

Ryan E Pavlovicz, Hahnbeom Park, Frank DiMaio
<span title="2020-09-21">2020</span> <i title="Public Library of Science"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
We introduce an updated energy model that efficiently captures the energetic effects of these ordered water molecules on the surfaces of proteins.  ...  We show that our new approach and energy model yield significant improvements in native structure recovery of protein-protein and protein-ligand docking discrimination tests.  ...  Acknowledgments This work was facilitated though the use of advanced computational, storage, and networking infrastructure provided by the Hyak supercomputer system at the University of Washington.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1008103">doi:10.1371/journal.pcbi.1008103</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32956350">pmid:32956350</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7529342/">pmcid:PMC7529342</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q3kgjgt2m5egnauk7drbofyy2e">fatcat:q3kgjgt2m5egnauk7drbofyy2e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200923032558/https://journals.plos.org/ploscompbiol/article/file?id=10.1371%2Fjournal.pcbi.1008103&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/e3/bb/e3bba8d3c4b56b786c46ca6ee82b5c0fac9d487d.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.1008103"> <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/PMC7529342" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Solvation Thermodynamics in Different Solvents – Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory

Johannes Kraml, Florian Hofer, Anna Sophia Kamenik, Franz Waibl, Ursula Kahler, Michael Schauperl, Klaus R. Liedl
<span title="2020-07-08">2020</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;
In this study, we introduce an extended version of the GIST algorithm, which enables the calculation for chloroform in addition to water.  ...  Grid Inhomogeneous Solvation Theory (GIST) facilitates the calculation of solvation free energy.  ...  , 40, 44 integration of solvation thermodynamics into structure−affinity relationships, 45 improvement of docking scoring functions, 46 and correlation of desolvation of aromatic moieties with binding  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jcim.0c00289">doi:10.1021/acs.jcim.0c00289</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32639731">pmid:32639731</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7460078/">pmcid:PMC7460078</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w5dykziturdbxko2paisprgswa">fatcat:w5dykziturdbxko2paisprgswa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220225123033/https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00289" 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/e0/78e0b51b477909446702954fd24746141f22ccc2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/acs.jcim.0c00289"> <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/PMC7460078" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An introduction to biomolecular simulations and docking

Cameron Mura, Charles E. McAnany
<span title="">2014</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ba36gjldcbcepllpy4cr33jkaq" style="color: black;">Molecular Simulation</a> </i> &nbsp;
This text introduces the physicochemical foundations of molecular simulations and docking, largely from the perspective of biomolecular interactions.  ...  to the diffusional dynamics and inter-molecular collisions in the early stages of formation of cellular-scale assemblies such as the ribosome.  ...  Acknowledgements This work is dedicated to the memory of Aubin Mura. We thank RG Bryant, CT  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/08927022.2014.935372">doi:10.1080/08927022.2014.935372</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/awr7ztftybc2zkylsoyz7f5sde">fatcat:awr7ztftybc2zkylsoyz7f5sde</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302185936/http://pdfs.semanticscholar.org/a800/25842924571b83a3215cfae2e5baa3cec029.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/a8/00/a80025842924571b83a3215cfae2e5baa3cec029.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/08927022.2014.935372"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> tandfonline.com </button> </a>

Intuitive, but not simple: Including explicit water molecules in protein-protein docking simulations improves model quality

Hardik I. Parikh, Glen E. Kellogg
<span title="2013-12-09">2013</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;
The HINT water Relevance metric identified the 'truly' bridging waters at the 30 protein-protein interfaces and we utilized them in "solvated" docking by manually inserting them into the input files for  ...  In this work, the Hydropathic INTeractions (HINT) force field model was used for scoring docked models in a data set of 30 high-resolution crystallographically characterized "dry" protein-protein complexes  ...  Acknowledgments We gratefully acknowledge the technical and philosophical assistance and advice of our  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24466">doi:10.1002/prot.24466</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24214407">pmid:24214407</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ayc3jpd62vfmngjyhsqsotjsse">fatcat:ayc3jpd62vfmngjyhsqsotjsse</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428121919/https://scholarscompass.vcu.edu/cgi/viewcontent.cgi?article=1014&amp;context=medc_pubs" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f5/3e/f53ea6cbc044f4f133293ff87fed84e150fac59c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/prot.24466"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Improvements to the APBS biomolecular solvation software suite

Elizabeth Jurrus, Dave Engel, Keith Star, Kyle Monson, Juan Brandi, Lisa E. Felberg, David H. Brookes, Leighton Wilson, Jiahui Chen, Karina Liles, Minju Chun, Peter Li (+12 others)
<span title="2017-10-24">2017</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bubxfqklvdwthsc43yvjbtjae" style="color: black;">Protein Science</a> </i> &nbsp;
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad  ...  APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust  ...  Acknowledgments The authors gratefully acknowledge NIH grant GM069702 for support of APBS and PDB2-PQR. PNNL is operated by Battelle for the U.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.3280">doi:10.1002/pro.3280</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28836357">pmid:28836357</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nuodvkqlfnah7evd4nurqv6h3a">fatcat:nuodvkqlfnah7evd4nurqv6h3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428045509/https://deepblue.lib.umich.edu/bitstream/handle/2027.42/141870/pro3280_am.pdf;jsessionid=B090835237D95E6E1CF2909E9D2F37CC?sequence=1" 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/4e/b0/4eb02587a5df1a174d4a8033ca6b9d89b9202d88.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pro.3280"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Differential Geometry-Based Solvation and Electrolyte Transport Models for Biomolecular Modeling: A Review [chapter]

Guo Wei, Nathan Baker
<span title="2016-03-14">2016</span> <i title="Pan Stanford"> Many-Body Effects and Electrostatics in Biomolecules </i> &nbsp;
This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade.  ...  Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current  ...  The authors are indebted to their collaborators who have contributed to the DG-based biomolecular modeling. Literature cited  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1201/b21343-15">doi:10.1201/b21343-15</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h3gkx3nopnemnd24ldjg7pa44e">fatcat:h3gkx3nopnemnd24ldjg7pa44e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302091247/http://pdfs.semanticscholar.org/a0e2/18681cb469b626e3527d7f36c94c29fedf44.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/a0/e2/a0e218681cb469b626e3527d7f36c94c29fedf44.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1201/b21343-15"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Protein-Protein Docking with Dynamic Residue Protonation States

Krishna Praneeth Kilambi, Kavan Reddy, Jeffrey J. Gray, James M. Briggs
<span title="2014-12-11">2014</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 this work, we present a pHsensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys) on-the-fly during the docking simulation  ...  . pHDock produces successful local docking funnels in approximately half (79/161) the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control  ...  Acknowledgments We thank all the developers of the Rosetta biomolecular modeling suite, which provided the backbone framework for the study. Author Contributions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1004018">doi:10.1371/journal.pcbi.1004018</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25501663">pmid:25501663</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4263365/">pmcid:PMC4263365</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rfplmcxg4vcxlnxgdji7ufh5au">fatcat:rfplmcxg4vcxlnxgdji7ufh5au</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015144903/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004018&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/ca/63/ca630905fb2a6e46beb85a0fa82e963280310028.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1004018"> <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/PMC4263365" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Machine Learning Implicit Solvation for Molecular Dynamics [article]

Yaoyi Chen, Andreas Krämer, Nicholas E. Charron, Brooke E. Husic, Cecilia Clementi, Frank Noé
<span title="2021-06-14">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Following the previous ML--CG models CGnet and CGSchnet, we introduce ISSNet, a graph neural network, to model the implicit solvent potential of mean force.  ...  We compare the solute conformational distributions under different solvation treatments for two peptide systems.  ...  62 for the parameterization of CG water models for ice-water mixture 63 and liquid water systems, 64 and for the computation of generalized Born radii in implicit solvent simulations. 65 The latter  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2106.07492v1">arXiv:2106.07492v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dlettevcxjdh5l6g56226htfgu">fatcat:dlettevcxjdh5l6g56226htfgu</a> </span>
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