{"id":"https://openalex.org/W2174856824","doi":"https://doi.org/10.1021/ci049784g","title":"Structure, Dynamics and Solvation of HIV-1 Protease/Saquinavir Complex in Aqueous Solution and Their Contributions to Drug Resistance:\u2009 Molecular Dynamic Simulations","display_name":"Structure, Dynamics and Solvation of HIV-1 Protease/Saquinavir Complex in Aqueous Solution and Their Contributions to Drug Resistance:\u2009 Molecular Dynamic Simulations","publication_year":2005,"publication_date":"2005-02-16","ids":{"openalex":"https://openalex.org/W2174856824","doi":"https://doi.org/10.1021/ci049784g","mag":"2174856824","pmid":"https://pubmed.ncbi.nlm.nih.gov/15807491"},"language":"en","primary_location":{"id":"doi:10.1021/ci049784g","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci049784g","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/A5043774189","display_name":"Kitiyaporn Wittayanarakul","orcid":null},"institutions":[{"id":"https://openalex.org/I129496196","display_name":"University of the Thai Chamber of Commerce","ror":"https://ror.org/03m7a5q02","country_code":"TH","type":"education","lineage":["https://openalex.org/I129496196"]},{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Kitiyaporn Wittayanarakul","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand","institution_ids":["https://openalex.org/I129496196","https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016996184","display_name":"Ornjira Aruksakunwong","orcid":null},"institutions":[{"id":"https://openalex.org/I129496196","display_name":"University of the Thai Chamber of Commerce","ror":"https://ror.org/03m7a5q02","country_code":"TH","type":"education","lineage":["https://openalex.org/I129496196"]},{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Ornjira Aruksakunwong","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand","institution_ids":["https://openalex.org/I129496196","https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080448599","display_name":"Pornthep Sompornpisut","orcid":"https://orcid.org/0000-0002-8029-332X"},"institutions":[{"id":"https://openalex.org/I129496196","display_name":"University of the Thai Chamber of Commerce","ror":"https://ror.org/03m7a5q02","country_code":"TH","type":"education","lineage":["https://openalex.org/I129496196"]},{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Pornthep Sompornpisut","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand","institution_ids":["https://openalex.org/I129496196","https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089269319","display_name":"Vannajan Sanghiran Lee","orcid":"https://orcid.org/0000-0002-2911-7726"},"institutions":[{"id":"https://openalex.org/I129496196","display_name":"University of the Thai Chamber of Commerce","ror":"https://ror.org/03m7a5q02","country_code":"TH","type":"education","lineage":["https://openalex.org/I129496196"]},{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Vannajan Sanghiran-Lee","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand","institution_ids":["https://openalex.org/I129496196","https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033605401","display_name":"Vudhichai Parasuk","orcid":"https://orcid.org/0000-0002-9990-2092"},"institutions":[{"id":"https://openalex.org/I129496196","display_name":"University of the Thai Chamber of Commerce","ror":"https://ror.org/03m7a5q02","country_code":"TH","type":"education","lineage":["https://openalex.org/I129496196"]},{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Vudhichai Parasuk","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand","institution_ids":["https://openalex.org/I129496196","https://openalex.org/I158708052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057334181","display_name":"Surapong Pinitglang","orcid":null},"institutions":[{"id":"https://openalex.org/I129496196","display_name":"University of the Thai Chamber of Commerce","ror":"https://ror.org/03m7a5q02","country_code":"TH","type":"education","lineage":["https://openalex.org/I129496196"]},{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Surapong Pinitglang","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand","institution_ids":["https://openalex.org/I129496196","https://openalex.org/I158708052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020458772","display_name":"Supot Hannongbua","orcid":"https://orcid.org/0000-0001-9008-2748"},"institutions":[{"id":"https://openalex.org/I129496196","display_name":"University of the Thai Chamber of Commerce","ror":"https://ror.org/03m7a5q02","country_code":"TH","type":"education","lineage":["https://openalex.org/I129496196"]},{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Supot Hannongbua","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Chulalongkorn University, Prathumwan, Bangkok 10330, Thailand, Department of Chemistry, Faculty of Science, Chiangmai University, Chiang Mai 50200, Thailand, and Department of Food Technology, Faculty of Science, The University of the Thai Chamber of Commerce, Dindang, Bangkok 10400, Thailand","institution_ids":["https://openalex.org/I129496196","https://openalex.org/I158708052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5152,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.59138991,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"45","issue":"2","first_page":"300","last_page":"308"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998999834060669,"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"}},{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9998999834060669,"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":0.9940000176429749,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/saquinavir","display_name":"Saquinavir","score":0.9766035079956055},{"id":"https://openalex.org/keywords/hiv-1-protease","display_name":"HIV-1 protease","score":0.6938703060150146},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6828026175498962},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6824962496757507},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.6372735500335693},{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.5866546630859375},{"id":"https://openalex.org/keywords/active-site","display_name":"Active site","score":0.45356982946395874},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.42117515206336975},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4173436164855957},{"id":"https://openalex.org/keywords/protease","display_name":"Protease","score":0.41603440046310425},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.24239543080329895},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.2397020161151886},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21396520733833313},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.1714726686477661},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.10601693391799927},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09706917405128479},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.08251485228538513}],"concepts":[{"id":"https://openalex.org/C2776937687","wikidata":"https://www.wikidata.org/wiki/Q422654","display_name":"Saquinavir","level":5,"score":0.9766035079956055},{"id":"https://openalex.org/C2777583353","wikidata":"https://www.wikidata.org/wiki/Q410261","display_name":"HIV-1 protease","level":4,"score":0.6938703060150146},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6828026175498962},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6824962496757507},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.6372735500335693},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.5866546630859375},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.45356982946395874},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.42117515206336975},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4173436164855957},{"id":"https://openalex.org/C2776714187","wikidata":"https://www.wikidata.org/wiki/Q212410","display_name":"Protease","level":3,"score":0.41603440046310425},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.24239543080329895},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.2397020161151886},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21396520733833313},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.1714726686477661},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.10601693391799927},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09706917405128479},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.08251485228538513},{"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/C2993143319","wikidata":"https://www.wikidata.org/wiki/Q583050","display_name":"Antiretroviral therapy","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005609","descriptor_name":"Free Radicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005609","descriptor_name":"Free Radicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005609","descriptor_name":"Free Radicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012996","descriptor_name":"Solutions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012996","descriptor_name":"Solutions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012996","descriptor_name":"Solutions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017320","descriptor_name":"HIV Protease Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018583","descriptor_name":"Pliability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018583","descriptor_name":"Pliability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018583","descriptor_name":"Pliability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019258","descriptor_name":"Saquinavir","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019258","descriptor_name":"Saquinavir","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019258","descriptor_name":"Saquinavir","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019258","descriptor_name":"Saquinavir","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019258","descriptor_name":"Saquinavir","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019258","descriptor_name":"Saquinavir","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D024882","descriptor_name":"Drug Resistance, Viral","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci049784g","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci049784g","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:15807491","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15807491","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322614","display_name":"Thailand Research Fund","ror":"https://ror.org/03gd1bh37"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1515152102","https://openalex.org/W1604083167","https://openalex.org/W1972227391","https://openalex.org/W1976161355","https://openalex.org/W1976552031","https://openalex.org/W1984492947","https://openalex.org/W2000720848","https://openalex.org/W2007130448","https://openalex.org/W2015795498","https://openalex.org/W2018813359","https://openalex.org/W2071421333","https://openalex.org/W2079769193","https://openalex.org/W2104639107","https://openalex.org/W2105175831","https://openalex.org/W2122199548","https://openalex.org/W2142640685","https://openalex.org/W4231484789","https://openalex.org/W4235968347"],"related_works":["https://openalex.org/W2049250591","https://openalex.org/W2075211009","https://openalex.org/W2081300260","https://openalex.org/W3013282133","https://openalex.org/W2126525653","https://openalex.org/W2801493643","https://openalex.org/W2256372280","https://openalex.org/W4245621070","https://openalex.org/W2027368525","https://openalex.org/W2075748968"],"abstract_inverted_index":{"As":[0],"it":[1],"is":[2,206,277],"known":[3],"that":[4,77,195,247,309],"the":[5,8,12,19,38,44,51,84,99,109,115,124,128,148,156,173,179,189,196,200,214,231,240,272,281,285,298],"understanding":[6],"of":[7,11,43,83,106,111,114,162,172,188,192,270,289,294,301],"basic":[9],"properties":[10,42],"enzyme/inhibitor":[13],"complex":[14],"leads":[15],"directly":[16],"to":[17,33,98,103,120,123,139,213,245,260,297,308],"enhancing":[18],"capability":[20,262],"in":[21,50,108,127,199,263,280,292],"drug":[22,25,264,267],"designing":[23,265],"and":[24,40,59,61,67,79,168,219,225,234,251,266,287,305],"discovery.":[26],"Molecular":[27],"dynamics":[28],"simulations":[29],"have":[30],"been":[31],"performed":[32],"examine":[34],"detailed":[35],"information":[36],"on":[37,135,147,209],"structure":[39],"dynamical":[41],"HIV-1":[45,129,174,201,226],"PR":[46,130,175,202,227],"complexed":[47,203],"with":[48,144,204],"saquinavir":[49,167,205,224,302],"three":[52],"protonated":[53],"states,":[54,236],"monoprotonates":[55],"at":[56,64],"Asp25":[57,66],"(Mono-25)":[58],"Asp25'(Mono-25')":[60],"diprotonate":[62],"(Di-Pro)":[63],"both":[65],"Asp25'.":[68],"The":[69,132,183],"obtained":[70],"results":[71,184],"support":[72],"clinical":[73],"data":[74],"which":[75,276,310],"reveal":[76],"Ile84":[78,100,107],"Gly48":[80,116,133],"are":[81],"two":[82,241],"most":[85],"frequent":[86],"residues":[87,253],"where":[88],"mutation":[89,101,117],"toward":[90],"a":[91,169,258],"protease":[92],"inhibitor":[93,250],"takes":[94],"place.":[95],"In":[96,160,211,283],"contrast":[97,212],"due":[102,122],"high":[104],"displacement":[105],"presence":[110],"saquinavir,":[112,145],"source":[113],"was":[118,153,311],"observed":[119],"be":[121,255],"limited":[125],"space":[126],"pocket.":[131],"was,":[134],"one":[136],"side,":[137],"found":[138,229],"form":[140],"strong":[141],"hydrogen":[142,221,295],"bonds":[143,222],"while":[146],"other":[149],"side":[150],"this":[151],"residue":[152],"repelled":[154],"by":[155],"hydrophobic":[157],"Phe53":[158],"residue.":[159],"terms":[161,293],"inhibitor/enzyme":[163,274],"binding,":[164],"interactions":[165],"between":[166,223,239,249],"catalytic":[170,252],"triad":[171],"were":[176,228,303],"calculated":[177],"using":[178,271],"ab":[180],"initio":[181],"method.":[182],"show":[185],"an":[186],"order":[187],"binding":[190,215,288],"energy":[191],"Mono25<Di-pro<<Mono-25',":[193],"suggesting":[194],"active":[197],"site":[198],"monoprotonated":[207],"states":[208],"Asp25.":[210],"energy,":[216],"3,":[217],"6":[218],"12":[220],"for":[230],"Mono-25,":[232],"Mono-25'":[233],"Di-pro":[235],"respectively.":[237],"Discrepancy":[238],"trends":[242],"suggests":[243],"us":[244],"conclude":[246],"interaction":[248,275],"should":[254],"used":[256],"as":[257],"criteria":[259],"enhance":[261],"screening":[268],"instead":[269],"total":[273],"normally":[278],"reported":[279,312],"literature.":[282],"addition,":[284],"distribution":[286],"water":[290],"molecules,":[291],"bonding,":[296],"donor":[299],"atoms":[300],"investigated":[304],"discussed,":[306],"referring":[307],"experimentally.":[313]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
