{"id":"https://openalex.org/W1494651318","doi":"https://doi.org/10.1007/11875741_15","title":"Grid Assisted Ensemble Molecular Dynamics Simulations of HIV-1 Proteases Reveal Novel Conformations of the Inhibitor Saquinavir","display_name":"Grid Assisted Ensemble Molecular Dynamics Simulations of HIV-1 Proteases Reveal Novel Conformations of the Inhibitor Saquinavir","publication_year":2006,"publication_date":"2006-01-01","ids":{"openalex":"https://openalex.org/W1494651318","doi":"https://doi.org/10.1007/11875741_15","mag":"1494651318"},"language":"en","primary_location":{"id":"doi:10.1007/11875741_15","is_oa":false,"landing_page_url":"https://doi.org/10.1007/11875741_15","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"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":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"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/A5033516543","display_name":"S. Kashif Sadiq","orcid":"https://orcid.org/0000-0002-5112-0307"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"S. Kashif Sadiq","raw_affiliation_strings":["Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H 0AJ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H 0AJ","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046138213","display_name":"Stefan J. Zasada","orcid":"https://orcid.org/0000-0003-4643-4982"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stefan J. Zasada","raw_affiliation_strings":["Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H 0AJ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H 0AJ","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066453821","display_name":"Peter V. Coveney","orcid":"https://orcid.org/0000-0002-8787-7256"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter V. Coveney","raw_affiliation_strings":["Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H 0AJ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H 0AJ","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":2.1644,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.91053048,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"150","last_page":"161"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9979000091552734,"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/T10112","display_name":"HIV Research and Treatment","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/saquinavir","display_name":"Saquinavir","score":0.9108085036277771},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6807600855827332},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5444217920303345},{"id":"https://openalex.org/keywords/hiv-1-protease","display_name":"HIV-1 protease","score":0.4596182703971863},{"id":"https://openalex.org/keywords/protease","display_name":"Protease","score":0.4535291790962219},{"id":"https://openalex.org/keywords/protease-inhibitor","display_name":"Protease inhibitor (pharmacology)","score":0.44116461277008057},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.43911659717559814},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.41197603940963745},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.34760093688964844},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.31776732206344604},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.16422539949417114},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.1510278880596161},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13531461358070374}],"concepts":[{"id":"https://openalex.org/C2776937687","wikidata":"https://www.wikidata.org/wiki/Q422654","display_name":"Saquinavir","level":5,"score":0.9108085036277771},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6807600855827332},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5444217920303345},{"id":"https://openalex.org/C2777583353","wikidata":"https://www.wikidata.org/wiki/Q410261","display_name":"HIV-1 protease","level":4,"score":0.4596182703971863},{"id":"https://openalex.org/C2776714187","wikidata":"https://www.wikidata.org/wiki/Q212410","display_name":"Protease","level":3,"score":0.4535291790962219},{"id":"https://openalex.org/C2781143361","wikidata":"https://www.wikidata.org/wiki/Q55761529","display_name":"Protease inhibitor (pharmacology)","level":5,"score":0.44116461277008057},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.43911659717559814},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.41197603940963745},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.34760093688964844},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.31776732206344604},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.16422539949417114},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.1510278880596161},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13531461358070374},{"id":"https://openalex.org/C2993143319","wikidata":"https://www.wikidata.org/wiki/Q583050","display_name":"Antiretroviral therapy","level":4,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C142462285","wikidata":"https://www.wikidata.org/wiki/Q2528140","display_name":"Viral load","level":3,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"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/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/11875741_15","is_oa":false,"landing_page_url":"https://doi.org/10.1007/11875741_15","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"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":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:106387","is_oa":false,"landing_page_url":"http://discovery.ucl.ac.uk/106387/","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":"     In: Berthold, MR and Glen, R and Fischer, I, (eds.) COMPUTATIONAL LIFE SCIENCES II, PROCEEDINGS.  (pp. 150 - 161).  SPRINGER-VERLAG BERLIN (2006)     ","raw_type":"Proceedings paper"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.5699999928474426}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1965510413","https://openalex.org/W1969009510","https://openalex.org/W1976499671","https://openalex.org/W1981651833","https://openalex.org/W2019526592","https://openalex.org/W2029667189","https://openalex.org/W2035687084","https://openalex.org/W2049934777","https://openalex.org/W2085562576","https://openalex.org/W2103815459","https://openalex.org/W2105175831","https://openalex.org/W2106140689","https://openalex.org/W2114367386","https://openalex.org/W2116796748","https://openalex.org/W2123166384","https://openalex.org/W2129187661","https://openalex.org/W2131288855","https://openalex.org/W2147993766","https://openalex.org/W2271871949","https://openalex.org/W2311078281","https://openalex.org/W4236479494"],"related_works":["https://openalex.org/W2074816934","https://openalex.org/W2416022335","https://openalex.org/W2049250591","https://openalex.org/W2004500184","https://openalex.org/W2326728996","https://openalex.org/W2138042650","https://openalex.org/W2039665105","https://openalex.org/W2075211009","https://openalex.org/W2129496382","https://openalex.org/W2046433870"],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}