{"id":"https://openalex.org/W2075691196","doi":"https://doi.org/10.1021/ci200623n","title":"Conformational Free Energy Modeling of Druglike Molecules by Metadynamics in the WHIM Space","display_name":"Conformational Free Energy Modeling of Druglike Molecules by Metadynamics in the WHIM Space","publication_year":2012,"publication_date":"2012-02-23","ids":{"openalex":"https://openalex.org/W2075691196","doi":"https://doi.org/10.1021/ci200623n","mag":"2075691196","pmid":"https://pubmed.ncbi.nlm.nih.gov/22360151"},"language":"en","primary_location":{"id":"doi:10.1021/ci200623n","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200623n","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/A5068377776","display_name":"Vojt\u011bch Spiwok","orcid":"https://orcid.org/0000-0001-8108-2033"},"institutions":[{"id":"https://openalex.org/I207624831","display_name":"Slovak Academy of Sciences","ror":"https://ror.org/03h7qq074","country_code":"SK","type":"government","lineage":["https://openalex.org/I207624831"]},{"id":"https://openalex.org/I9073902","display_name":"University of Chemistry and Technology, Prague","ror":"https://ror.org/05ggn0a85","country_code":"CZ","type":"education","lineage":["https://openalex.org/I9073902"]}],"countries":["CZ","SK"],"is_corresponding":true,"raw_author_name":"Vojt\u011bch Spiwok","raw_affiliation_strings":["Department\rof Biochemistry and Microbiology, Institute of Chemical Technology Prague, Technick\u00e1 3, Prague\r6, 166 28, Czech Republic","Department\rof Structure and Function of Saccharides, Institute of\rChemistry, Center for Glycomics, Slovak Academy of Sciences, D\u00fabravsk\u00e1 cesta 9, Bratislava, 845 38, Slovak Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biochemistry and Microbiology, Institute of Chemical Technology Prague, Technick\u00e1 3, Prague\r6, 166 28, Czech Republic","institution_ids":["https://openalex.org/I9073902"]},{"raw_affiliation_string":"Department\rof Structure and Function of Saccharides, Institute of\rChemistry, Center for Glycomics, Slovak Academy of Sciences, D\u00fabravsk\u00e1 cesta 9, Bratislava, 845 38, Slovak Republic","institution_ids":["https://openalex.org/I207624831"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009698720","display_name":"Katar\u00edna Hlat-Glembov\u00e1","orcid":null},"institutions":[{"id":"https://openalex.org/I9073902","display_name":"University of Chemistry and Technology, Prague","ror":"https://ror.org/05ggn0a85","country_code":"CZ","type":"education","lineage":["https://openalex.org/I9073902"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Katar\u00edna Hlat-Glembov\u00e1","raw_affiliation_strings":["Department\rof Biochemistry and Microbiology, Institute of Chemical Technology Prague, Technick\u00e1 3, Prague\r6, 166 28, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biochemistry and Microbiology, Institute of Chemical Technology Prague, Technick\u00e1 3, Prague\r6, 166 28, Czech Republic","institution_ids":["https://openalex.org/I9073902"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006856491","display_name":"Igor Tvaro\u0161ka","orcid":"https://orcid.org/0000-0003-2740-944X"},"institutions":[{"id":"https://openalex.org/I207624831","display_name":"Slovak Academy of Sciences","ror":"https://ror.org/03h7qq074","country_code":"SK","type":"government","lineage":["https://openalex.org/I207624831"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Igor Tvaro\u0161ka","raw_affiliation_strings":["Department\rof Structure and Function of Saccharides, Institute of\rChemistry, Center for Glycomics, Slovak Academy of Sciences, D\u00fabravsk\u00e1 cesta 9, Bratislava, 845 38, Slovak Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Structure and Function of Saccharides, Institute of\rChemistry, Center for Glycomics, Slovak Academy of Sciences, D\u00fabravsk\u00e1 cesta 9, Bratislava, 845 38, Slovak Republic","institution_ids":["https://openalex.org/I207624831"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026087774","display_name":"Blanka Kr\u00e1lov\u00e1","orcid":"https://orcid.org/0000-0001-8954-5872"},"institutions":[{"id":"https://openalex.org/I9073902","display_name":"University of Chemistry and Technology, Prague","ror":"https://ror.org/05ggn0a85","country_code":"CZ","type":"education","lineage":["https://openalex.org/I9073902"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Blanka Kr\u00e1lov\u00e1","raw_affiliation_strings":["Department\rof Biochemistry and Microbiology, Institute of Chemical Technology Prague, Technick\u00e1 3, Prague\r6, 166 28, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biochemistry and Microbiology, Institute of Chemical Technology Prague, Technick\u00e1 3, Prague\r6, 166 28, Czech Republic","institution_ids":["https://openalex.org/I9073902"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5068377776"],"corresponding_institution_ids":["https://openalex.org/I207624831","https://openalex.org/I9073902"],"apc_list":null,"apc_paid":null,"fwci":0.5297,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.65322541,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"52","issue":"3","first_page":"804","last_page":"813"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9909999966621399,"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":0.9909999966621399,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9509999752044678,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10913","display_name":"Molecular Junctions and Nanostructures","score":0.9315999746322632,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metadynamics","display_name":"Metadynamics","score":0.9730663299560547},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6352781057357788},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6072553992271423},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.573248028755188},{"id":"https://openalex.org/keywords/free-energy-perturbation","display_name":"Free energy perturbation","score":0.5019984245300293},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"Energy landscape","score":0.429270476102829},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4291996955871582},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.37262314558029175},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.3393769860267639}],"concepts":[{"id":"https://openalex.org/C62752575","wikidata":"https://www.wikidata.org/wiki/Q6822487","display_name":"Metadynamics","level":3,"score":0.9730663299560547},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6352781057357788},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6072553992271423},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.573248028755188},{"id":"https://openalex.org/C162641036","wikidata":"https://www.wikidata.org/wiki/Q5500215","display_name":"Free energy perturbation","level":3,"score":0.5019984245300293},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.429270476102829},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4291996955871582},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.37262314558029175},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3393769860267639},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","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}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200623n","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200623n","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:22360151","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22360151","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":[{"score":0.8899999856948853,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1532848864","https://openalex.org/W1591081957","https://openalex.org/W1966078827","https://openalex.org/W1976161355","https://openalex.org/W1976499671","https://openalex.org/W1986986500","https://openalex.org/W1998264260","https://openalex.org/W2010311152","https://openalex.org/W2033845865","https://openalex.org/W2035266068","https://openalex.org/W2057477511","https://openalex.org/W2057980421","https://openalex.org/W2060341378","https://openalex.org/W2061938171","https://openalex.org/W2066951434","https://openalex.org/W2067174909","https://openalex.org/W2076790509","https://openalex.org/W2077412035","https://openalex.org/W2089449476","https://openalex.org/W2091283009","https://openalex.org/W2099789127","https://openalex.org/W2107841008","https://openalex.org/W2114367386","https://openalex.org/W2125814404","https://openalex.org/W2126559590","https://openalex.org/W2128572087","https://openalex.org/W2132589721","https://openalex.org/W2137137488","https://openalex.org/W2137601120","https://openalex.org/W2144288821","https://openalex.org/W2147993766","https://openalex.org/W2149655632","https://openalex.org/W2152629484","https://openalex.org/W2168030379","https://openalex.org/W2319760302","https://openalex.org/W4213151958"],"related_works":["https://openalex.org/W2584653976","https://openalex.org/W2020879467","https://openalex.org/W2124175595","https://openalex.org/W2913188753","https://openalex.org/W2953107349","https://openalex.org/W4220878319","https://openalex.org/W1972594892","https://openalex.org/W2153865022","https://openalex.org/W2023483669","https://openalex.org/W2075691196"],"abstract_inverted_index":{"Protein-ligand":[0],"affinities":[1],"can":[2],"be":[3],"significantly":[4],"influenced":[5],"not":[6],"only":[7],"by":[8,14,60,111,140],"the":[9,68,144],"interaction":[10],"itself":[11],"but":[12],"also":[13],"conformational":[15,29,48,81,137],"equilibrium":[16],"of":[17,27,31,36,52,70,78,96,106,114,120,124,132,136],"both":[18],"binding":[19,142],"partners,":[20],"free":[21,24,49,94,100,121,125,133],"ligand":[22,33,43],"and":[23,34,89,103,126],"protein.":[25],"Identification":[26],"important":[28,40],"families":[30],"a":[32,63,112],"prediction":[35],"their":[37],"thermodynamics":[38],"is":[39],"for":[41],"efficient":[42],"design.":[44],"Here":[45],"we":[46],"report":[47],"energy":[50,101,122,134],"modeling":[51],"nine":[53],"small-molecule":[54],"drugs":[55],"in":[56,67],"explicitly":[57],"modeled":[58],"water":[59],"metadynamics":[61,79],"with":[62],"bias":[64],"potential":[65],"applied":[66],"space":[69],"weighted":[71],"holistic":[72],"invariant":[73],"molecular":[74,86,116],"(WHIM)":[75],"descriptors.":[76],"Application":[77],"enhances":[80],"sampling":[82],"compared":[83],"to":[84,91,143],"unbiased":[85,115],"dynamics":[87,117],"simulation":[88],"allows":[90],"predict":[92],"relative":[93],"energies":[95],"key":[97],"conformations.":[98],"Selected":[99],"minima":[102],"one":[104],"example":[105],"transition":[107],"state":[108],"were":[109],"tested":[110],"series":[113],"simulation.":[118],"Comparison":[119],"surfaces":[123],"target-bound":[127],"Imatinib":[128],"provides":[129],"an":[130],"estimate":[131],"penalty":[135],"change":[138],"induced":[139],"its":[141],"target.":[145]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
