{"id":"https://openalex.org/W2072543428","doi":"https://doi.org/10.1023/b:jcam.0000021883.44532.75","title":"Molecular dynamics simulation of Matrix Metalloproteinase 2: fluctuations and time evolution of recognition pockets","display_name":"Molecular dynamics simulation of Matrix Metalloproteinase 2: fluctuations and time evolution of recognition pockets","publication_year":2003,"publication_date":"2003-12-01","ids":{"openalex":"https://openalex.org/W2072543428","doi":"https://doi.org/10.1023/b:jcam.0000021883.44532.75","mag":"2072543428","pmid":"https://pubmed.ncbi.nlm.nih.gov/15124932"},"language":"en","primary_location":{"id":"doi:10.1023/b:jcam.0000021883.44532.75","is_oa":false,"landing_page_url":"https://doi.org/10.1023/b:jcam.0000021883.44532.75","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/A5018585630","display_name":"Mattia Falconi","orcid":"https://orcid.org/0000-0002-3990-4758"},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mattia Falconi","raw_affiliation_strings":["INFM and Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1-00133 Rome, Italy","INFM and Department of Biology, University of Rome \u201cTor Vergata,\u201d Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INFM and Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1-00133 Rome, Italy","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"INFM and Department of Biology, University of Rome \u201cTor Vergata,\u201d Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023715173","display_name":"Gioia Altobelli","orcid":"https://orcid.org/0000-0001-9338-3466"},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gioia Altobelli","raw_affiliation_strings":["INFM and Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, I-00133, Rome, Italy","INFM and Department of Biology, University of Rome \u201cTor Vergata,\u201d Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INFM and Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, I-00133, Rome, Italy","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"INFM and Department of Biology, University of Rome \u201cTor Vergata,\u201d Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027605693","display_name":"Maria Cristina Iovino","orcid":null},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Maria Cristina Iovino","raw_affiliation_strings":["INFM and Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, I-00133, Rome, Italy","INFM and Department of Biology, University of Rome \u201cTor Vergata,\u201d Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INFM and Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, I-00133, Rome, Italy","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"INFM and Department of Biology, University of Rome \u201cTor Vergata,\u201d Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019739693","display_name":"V. Politi","orcid":null},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Vincenzo Politi","raw_affiliation_strings":["Polifarma S.p.A., Via di Tor Sapienza 138, I-00155, Rome, Italy","Polifarma S.p.A., Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Polifarma S.p.A., Via di Tor Sapienza 138, I-00155, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]},{"raw_affiliation_string":"Polifarma S.p.A., Rome, Italy","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019534523","display_name":"Alessandro Desideri","orcid":"https://orcid.org/0000-0003-1541-4217"},"institutions":[{"id":"https://openalex.org/I116067653","display_name":"University of Rome Tor Vergata","ror":"https://ror.org/02p77k626","country_code":"IT","type":"education","lineage":["https://openalex.org/I116067653"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessandro Desideri","raw_affiliation_strings":["INFM and Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, I-00133, Rome, Italy","INFM and Department of Biology, University of Rome \u201cTor Vergata,\u201d Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INFM and Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, I-00133, Rome, Italy","institution_ids":["https://openalex.org/I116067653"]},{"raw_affiliation_string":"INFM and Department of Biology, University of Rome \u201cTor Vergata,\u201d Rome, Italy","institution_ids":["https://openalex.org/I116067653"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":0.3955,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.62800116,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"17","issue":"12","first_page":"837","last_page":"848"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10620","display_name":"Protease and Inhibitor Mechanisms","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10620","display_name":"Protease and Inhibitor Mechanisms","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T12620","display_name":"Signaling Pathways in Disease","score":0.9790999889373779,"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":0.9706000089645386,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7076383233070374},{"id":"https://openalex.org/keywords/matrix-metalloproteinase","display_name":"Matrix metalloproteinase","score":0.6680166721343994},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5756199359893799},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.4994049072265625},{"id":"https://openalex.org/keywords/metalloproteinase","display_name":"Metalloproteinase","score":0.48789024353027344},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.43815919756889343},{"id":"https://openalex.org/keywords/matrix-metalloproteinase-3","display_name":"Matrix Metalloproteinase 3","score":0.41378456354141235},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3928205370903015},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.37636837363243103},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35247689485549927},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3225845694541931},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.28496426343917847},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.2841591238975525},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.23565798997879028},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.20769864320755005},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.187218576669693},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.17532864212989807},{"id":"https://openalex.org/keywords/composite-material","display_name":"Composite material","score":0.07801815867424011}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7076383233070374},{"id":"https://openalex.org/C109523444","wikidata":"https://www.wikidata.org/wiki/Q424216","display_name":"Matrix metalloproteinase","level":2,"score":0.6680166721343994},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5756199359893799},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.4994049072265625},{"id":"https://openalex.org/C55728118","wikidata":"https://www.wikidata.org/wiki/Q425402","display_name":"Metalloproteinase","level":3,"score":0.48789024353027344},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.43815919756889343},{"id":"https://openalex.org/C2910007452","wikidata":"https://www.wikidata.org/wiki/Q21114943","display_name":"Matrix Metalloproteinase 3","level":3,"score":0.41378456354141235},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3928205370903015},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.37636837363243103},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35247689485549927},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3225845694541931},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.28496426343917847},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2841591238975525},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.23565798997879028},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.20769864320755005},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.187218576669693},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.17532864212989807},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.07801815867424011},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003094","descriptor_name":"Collagen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003094","descriptor_name":"Collagen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003094","descriptor_name":"Collagen","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003094","descriptor_name":"Collagen","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003094","descriptor_name":"Collagen","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003094","descriptor_name":"Collagen","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014961","descriptor_name":"X-Ray Diffraction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014961","descriptor_name":"X-Ray Diffraction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014961","descriptor_name":"X-Ray Diffraction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020778","descriptor_name":"Matrix Metalloproteinase 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020778","descriptor_name":"Matrix Metalloproteinase 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020778","descriptor_name":"Matrix Metalloproteinase 2","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020778","descriptor_name":"Matrix Metalloproteinase 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020778","descriptor_name":"Matrix Metalloproteinase 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020778","descriptor_name":"Matrix Metalloproteinase 2","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1023/b:jcam.0000021883.44532.75","is_oa":false,"landing_page_url":"https://doi.org/10.1023/b:jcam.0000021883.44532.75","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:15124932","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15124932","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},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1379114","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/1379114/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN , 17  (12)   pp. 837-848.   (2003)      ","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6800000071525574,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1511364405","https://openalex.org/W1520127302","https://openalex.org/W1964556609","https://openalex.org/W1964613779","https://openalex.org/W1970747580","https://openalex.org/W1979221090","https://openalex.org/W1984483611","https://openalex.org/W2000831618","https://openalex.org/W2004360551","https://openalex.org/W2008708467","https://openalex.org/W2011282929","https://openalex.org/W2013215928","https://openalex.org/W2026423508","https://openalex.org/W2035687084","https://openalex.org/W2041902442","https://openalex.org/W2043810400","https://openalex.org/W2049475242","https://openalex.org/W2055758035","https://openalex.org/W2056274186","https://openalex.org/W2059919196","https://openalex.org/W2062351773","https://openalex.org/W2091563009","https://openalex.org/W2106140689","https://openalex.org/W2110308836","https://openalex.org/W2130479394","https://openalex.org/W2138871907","https://openalex.org/W2147145439","https://openalex.org/W2151523705","https://openalex.org/W4299790875"],"related_works":["https://openalex.org/W2974627606","https://openalex.org/W2091009027","https://openalex.org/W1936396226","https://openalex.org/W2088172329","https://openalex.org/W3015815503","https://openalex.org/W2152806358","https://openalex.org/W4376595826","https://openalex.org/W1993786592","https://openalex.org/W1156698136","https://openalex.org/W4241582355"],"abstract_inverted_index":null,"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}