{"id":"https://openalex.org/W2042443692","doi":"https://doi.org/10.1021/ci500296f","title":"Protein\u2013Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials","display_name":"Protein\u2013Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials","publication_year":2014,"publication_date":"2014-05-24","ids":{"openalex":"https://openalex.org/W2042443692","doi":"https://doi.org/10.1021/ci500296f","mag":"2042443692","pmid":"https://pubmed.ncbi.nlm.nih.gov/24855894"},"language":"en","primary_location":{"id":"doi:10.1021/ci500296f","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500296f","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045389502","display_name":"Manuel P. Luitz","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Manuel P. Luitz","raw_affiliation_strings":["Physik-Department\rT38, Technische Universit\u00e4t M\u00fcnchen, James Franck Str. 1, 85748 Garching, Germany"],"affiliations":[{"raw_affiliation_string":"Physik-Department\rT38, Technische Universit\u00e4t M\u00fcnchen, James Franck Str. 1, 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090330416","display_name":"Martin Zacharias","orcid":"https://orcid.org/0000-0001-5163-2663"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Zacharias","raw_affiliation_strings":["Physik-Department\rT38, Technische Universit\u00e4t M\u00fcnchen, James Franck Str. 1, 85748 Garching, Germany"],"affiliations":[{"raw_affiliation_string":"Physik-Department\rT38, Technische Universit\u00e4t M\u00fcnchen, James Franck Str. 1, 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045389502"],"corresponding_institution_ids":["https://openalex.org/I62916508"],"apc_list":null,"apc_paid":null,"fwci":2.3704,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.88839804,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"54","issue":"6","first_page":"1669","last_page":"1675"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/replica","display_name":"Replica","score":0.781598687171936},{"id":"https://openalex.org/keywords/searching-the-conformational-space-for-docking","display_name":"Searching the conformational space for docking","score":0.7641043663024902},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7372830510139465},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.656245768070221},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.6470330357551575},{"id":"https://openalex.org/keywords/hamiltonian","display_name":"Hamiltonian (control theory)","score":0.5246260762214661},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.5239670276641846},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5159781575202942},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5105689764022827},{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.5029763579368591},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.4465939402580261},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.4351107180118561},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.36875927448272705},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3527650833129883},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.32745951414108276},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3051770031452179},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.2854326367378235},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.24467059969902039},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1682186722755432},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.14301076531410217},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.11251357197761536},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.08536019921302795}],"concepts":[{"id":"https://openalex.org/C2775937380","wikidata":"https://www.wikidata.org/wiki/Q1232589","display_name":"Replica","level":2,"score":0.781598687171936},{"id":"https://openalex.org/C44695244","wikidata":"https://www.wikidata.org/wiki/Q7441727","display_name":"Searching the conformational space for docking","level":3,"score":0.7641043663024902},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7372830510139465},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.656245768070221},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.6470330357551575},{"id":"https://openalex.org/C130787639","wikidata":"https://www.wikidata.org/wiki/Q5645293","display_name":"Hamiltonian (control theory)","level":2,"score":0.5246260762214661},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.5239670276641846},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5159781575202942},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5105689764022827},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.5029763579368591},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.4465939402580261},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.4351107180118561},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.36875927448272705},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3527650833129883},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.32745951414108276},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3051770031452179},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.2854326367378235},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.24467059969902039},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1682186722755432},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.14301076531410217},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.11251357197761536},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.08536019921302795},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006183","descriptor_name":"H-2 Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006183","descriptor_name":"H-2 Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006183","descriptor_name":"H-2 Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006183","descriptor_name":"H-2 Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006183","descriptor_name":"H-2 Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006183","descriptor_name":"H-2 Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022021","descriptor_name":"Tacrolimus Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D022021","descriptor_name":"Tacrolimus Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D022021","descriptor_name":"Tacrolimus Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D022021","descriptor_name":"Tacrolimus Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022021","descriptor_name":"Tacrolimus Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022021","descriptor_name":"Tacrolimus Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022061","descriptor_name":"Tacrolimus Binding Protein 1A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D022061","descriptor_name":"Tacrolimus Binding Protein 1A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D022061","descriptor_name":"Tacrolimus Binding Protein 1A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D022061","descriptor_name":"Tacrolimus Binding Protein 1A","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022061","descriptor_name":"Tacrolimus Binding Protein 1A","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022061","descriptor_name":"Tacrolimus Binding Protein 1A","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci500296f","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500296f","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:24855894","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24855894","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8700000047683716}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320331625","display_name":"Gauss Centre for Supercomputing","ror":"https://ror.org/0585fsj26"},{"id":"https://openalex.org/F4320336863","display_name":"Leibniz-Rechenzentrum","ror":"https://ror.org/05558nw16"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1592950931","https://openalex.org/W1964692994","https://openalex.org/W1966078827","https://openalex.org/W1967582433","https://openalex.org/W1976499671","https://openalex.org/W1982306719","https://openalex.org/W1984481443","https://openalex.org/W1987100568","https://openalex.org/W1989814214","https://openalex.org/W1995907662","https://openalex.org/W2001425282","https://openalex.org/W2007584318","https://openalex.org/W2007905703","https://openalex.org/W2015688756","https://openalex.org/W2028930733","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2036527573","https://openalex.org/W2049617698","https://openalex.org/W2051532262","https://openalex.org/W2057477511","https://openalex.org/W2065908318","https://openalex.org/W2068190879","https://openalex.org/W2070915333","https://openalex.org/W2077954341","https://openalex.org/W2081693079","https://openalex.org/W2083995470","https://openalex.org/W2087795016","https://openalex.org/W2089188080","https://openalex.org/W2099630507","https://openalex.org/W2101874060","https://openalex.org/W2106449489","https://openalex.org/W2107572441","https://openalex.org/W2127290087","https://openalex.org/W2128572087","https://openalex.org/W2129954993","https://openalex.org/W2133620840","https://openalex.org/W2144288821","https://openalex.org/W2147993766","https://openalex.org/W2153983456","https://openalex.org/W2155554859","https://openalex.org/W2156502139","https://openalex.org/W2159817444","https://openalex.org/W2171268876","https://openalex.org/W2419313274","https://openalex.org/W3102987216","https://openalex.org/W4238009417"],"related_works":["https://openalex.org/W1989505723","https://openalex.org/W1992786240","https://openalex.org/W4246463539","https://openalex.org/W4213013656","https://openalex.org/W4235673852","https://openalex.org/W2037320233","https://openalex.org/W4310018788","https://openalex.org/W3043968438","https://openalex.org/W2951473524","https://openalex.org/W1997409847"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1],"(MD)":[2],"simulations":[3],"in":[4,27,41,112,139,148],"explicit":[5,21],"solvent":[6],"allow":[7],"studying":[8],"receptor-ligand":[9,96],"binding":[10,17,45,117,137,142,149],"processes":[11],"including":[12],"full":[13],"flexibility":[14],"of":[15,23,59,81,88],"the":[16,30,57,72,79,82,89,108,115],"partners":[18],"and":[19,74,98,134],"an":[20,33],"inclusion":[22],"solvation":[24],"effects.":[25],"However,":[26],"MD":[28,124],"simulations,":[29],"search":[31],"for":[32],"optimal":[34],"ligand-receptor":[35,61,69],"complex":[36],"geometry":[37,118],"is":[38,64],"frequently":[39],"trapped":[40],"locally":[42],"stable":[43],"non-native":[44],"geometries.":[46],"A":[47],"Hamiltonian":[48],"replica-exchange":[49],"(H-REMD)-based":[50],"protocol":[51],"has":[52,91],"been":[53,92],"designed":[54],"to":[55,132],"enhance":[56],"sampling":[58],"putative":[60],"complexes.":[62],"It":[63],"based":[65],"on":[66,94],"softening":[67],"nonbonded":[68],"interactions":[70],"along":[71],"replicas":[73],"one":[75,99],"reference":[76],"replica":[77],"under":[78],"control":[80],"original":[83],"force":[84],"field.":[85],"The":[86,126],"efficiency":[87],"method":[90,110],"evaluated":[93],"two":[95],"systems":[97],"protein-peptide":[100],"complex.":[101],"Starting":[102],"from":[103],"misplaced":[104],"initial":[105],"docking":[106],"geometries,":[107],"H-REMD":[109],"reached":[111],"each":[113],"case":[114],"known":[116],"significantly":[119],"faster":[120],"than":[121],"a":[122,140],"standard":[123],"simulation.":[125],"approach":[127],"could":[128],"also":[129],"be":[130],"useful":[131],"identify":[133],"evaluate":[135],"alternative":[136],"geometries":[138],"given":[141],"region":[143],"with":[144],"small":[145],"relative":[146],"differences":[147],"free":[150],"energy.":[151]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}