{"id":"https://openalex.org/W2034589527","doi":"https://doi.org/10.1007/s10822-011-9474-5","title":"Characterization of PDZ domain\u2013peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses","display_name":"Characterization of PDZ domain\u2013peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses","publication_year":2011,"publication_date":"2011-09-30","ids":{"openalex":"https://openalex.org/W2034589527","doi":"https://doi.org/10.1007/s10822-011-9474-5","mag":"2034589527","pmid":"https://pubmed.ncbi.nlm.nih.gov/21964565"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-011-9474-5","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-011-9474-5","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","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/A5100907689","display_name":"Feifei Tian","orcid":null},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I4800084","display_name":"Southwest Jiaotong University","ror":"https://ror.org/00hn7w693","country_code":"CN","type":"education","lineage":["https://openalex.org/I4800084"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Feifei Tian","raw_affiliation_strings":["Key Laboratory of Biorheological Science and Technology Under Ministry of Education, 111 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing 400044, China","Chongqing University","Southwest Jiaotong University"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Biorheological Science and Technology Under Ministry of Education, 111 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing 400044, China","institution_ids":[]},{"raw_affiliation_string":"Chongqing University","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"Southwest Jiaotong University","institution_ids":["https://openalex.org/I4800084"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082827291","display_name":"Yonggang Lv","orcid":"https://orcid.org/0000-0003-3966-8975"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yonggang Lv","raw_affiliation_strings":["Key Laboratory of Biorheological Science and Technology Under Ministry of Education, \u2018111\u2019 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing, 400044, China","Key Laboratory of Biorheological Science and Technology Under Ministry of Education, \u2018111\u2019 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Biorheological Science and Technology Under Ministry of Education, \u2018111\u2019 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing, 400044, China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"Key Laboratory of Biorheological Science and Technology Under Ministry of Education, \u2018111\u2019 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100438327","display_name":"Peng Zhou","orcid":"https://orcid.org/0000-0001-5681-9937"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peng Zhou","raw_affiliation_strings":["Center of Bioinformatics (COBI), School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China","Center of Bioinformatics (COBI), School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China"],"affiliations":[{"raw_affiliation_string":"Center of Bioinformatics (COBI), School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China","institution_ids":["https://openalex.org/I150229711"]},{"raw_affiliation_string":"Center of Bioinformatics (COBI), School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100784322","display_name":"Li Yang","orcid":"https://orcid.org/0000-0001-6589-7195"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Yang","raw_affiliation_strings":["Key Laboratory of Biorheological Science and Technology Under Ministry of Education, \u2018111\u2019 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing, 400044, China","Key Laboratory of Biorheological Science and Technology Under Ministry of Education, \u2018111\u2019 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Biorheological Science and Technology Under Ministry of Education, \u2018111\u2019 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing, 400044, China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"Key Laboratory of Biorheological Science and Technology Under Ministry of Education, \u2018111\u2019 Project Laboratory of Biomechanics and Tissue Repair, and Bioengineering College, Chongqing University, Chongqing, China","institution_ids":["https://openalex.org/I158842170"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100907689"],"corresponding_institution_ids":["https://openalex.org/I158842170","https://openalex.org/I4800084"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":1.1958,"has_fulltext":false,"cited_by_count":85,"citation_normalized_percentile":{"value":0.77511063,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"25","issue":"10","first_page":"947","last_page":"958"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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":0.9980999827384949,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9894000291824341,"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":0.974399983882904,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/pdz-domain","display_name":"PDZ domain","score":0.8962301015853882},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.6373090147972107},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6061592698097229},{"id":"https://openalex.org/keywords/entropy","display_name":"Entropy (arrow of time)","score":0.47063538432121277},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4389401972293854},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4188271462917328},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.40042489767074585},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3532543182373047},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.29011571407318115},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.23242652416229248},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.22848182916641235},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.15831652283668518},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13935518264770508}],"concepts":[{"id":"https://openalex.org/C154428179","wikidata":"https://www.wikidata.org/wiki/Q24721050","display_name":"PDZ domain","level":2,"score":0.8962301015853882},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6373090147972107},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6061592698097229},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.47063538432121277},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4389401972293854},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4188271462917328},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.40042489767074585},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3532543182373047},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.29011571407318115},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23242652416229248},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.22848182916641235},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.15831652283668518},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13935518264770508}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"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":"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":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054731","descriptor_name":"PDZ Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054731","descriptor_name":"PDZ Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054731","descriptor_name":"PDZ Domains","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":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-011-9474-5","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-011-9474-5","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:21964565","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21964565","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 computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8899999856948853}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1597773817","https://openalex.org/W1963744170","https://openalex.org/W1968344479","https://openalex.org/W1975580333","https://openalex.org/W1979715740","https://openalex.org/W1983142511","https://openalex.org/W1985446591","https://openalex.org/W1987451040","https://openalex.org/W1987704449","https://openalex.org/W2000933782","https://openalex.org/W2001029897","https://openalex.org/W2023272942","https://openalex.org/W2027528856","https://openalex.org/W2027978582","https://openalex.org/W2028826413","https://openalex.org/W2038767330","https://openalex.org/W2044940178","https://openalex.org/W2045185912","https://openalex.org/W2052033556","https://openalex.org/W2055546038","https://openalex.org/W2057482592","https://openalex.org/W2057664120","https://openalex.org/W2063092201","https://openalex.org/W2065989745","https://openalex.org/W2069123478","https://openalex.org/W2074570440","https://openalex.org/W2077973224","https://openalex.org/W2081831455","https://openalex.org/W2087548635","https://openalex.org/W2087719609","https://openalex.org/W2088365719","https://openalex.org/W2104230795","https://openalex.org/W2106648157","https://openalex.org/W2107713759","https://openalex.org/W2114512254","https://openalex.org/W2115291348","https://openalex.org/W2115339329","https://openalex.org/W2115815749","https://openalex.org/W2117925185","https://openalex.org/W2119821739","https://openalex.org/W2122199548","https://openalex.org/W2129386377","https://openalex.org/W2138652813","https://openalex.org/W2142873050","https://openalex.org/W2146038212","https://openalex.org/W2147463023","https://openalex.org/W2150155770","https://openalex.org/W2167361556","https://openalex.org/W4206257968","https://openalex.org/W4293003482","https://openalex.org/W4388166534"],"related_works":["https://openalex.org/W2913537206","https://openalex.org/W2014235532","https://openalex.org/W1981740764","https://openalex.org/W2275510245","https://openalex.org/W2207139036","https://openalex.org/W2162151490","https://openalex.org/W2066353226","https://openalex.org/W2115050780","https://openalex.org/W2132186283","https://openalex.org/W2064058502"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":17},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
