{"id":"https://openalex.org/W2103970104","doi":"https://doi.org/10.1109/cibcb.2008.4675772","title":"3D-Shape analysis of the HIV-1 protease ligand binding site","display_name":"3D-Shape analysis of the HIV-1 protease ligand binding site","publication_year":2008,"publication_date":"2008-09-01","ids":{"openalex":"https://openalex.org/W2103970104","doi":"https://doi.org/10.1109/cibcb.2008.4675772","mag":"2103970104"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2008.4675772","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2008.4675772","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","raw_type":"proceedings-article"},"type":"article","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/A5101959878","display_name":"Sunil Kumar","orcid":"https://orcid.org/0000-0001-6344-5750"},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sunil Kumar","raw_affiliation_strings":["The Electrical and Computer Engineering Department, San Diego State University, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"The Electrical and Computer Engineering Department, San Diego State University, San Diego, CA, USA","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022652844","display_name":"Rajni Garg","orcid":"https://orcid.org/0000-0002-9629-8141"},"institutions":[{"id":"https://openalex.org/I226560621","display_name":"California State University, San Marcos","ror":"https://ror.org/01j8e0j24","country_code":"US","type":"education","lineage":["https://openalex.org/I226560621"]},{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rajni Garg","raw_affiliation_strings":["Chemistry and Biochemistry Department, California State University, San Marcos, USA","Computational Science Research Center, San Diego State University, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Chemistry and Biochemistry Department, California State University, San Marcos, USA","institution_ids":["https://openalex.org/I226560621"]},{"raw_affiliation_string":"Computational Science Research Center, San Diego State University, San Diego, CA, USA","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068737983","display_name":"Srinivas R. Alla","orcid":null},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Srinivas R. Alla","raw_affiliation_strings":["Electrical and Computer Engineering Department, San Diego State University, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Department, San Diego State University, San Diego, CA, USA","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100419397","display_name":"Xiaoyu Zhang","orcid":"https://orcid.org/0000-0002-0951-9664"},"institutions":[{"id":"https://openalex.org/I226560621","display_name":"California State University, San Marcos","ror":"https://ror.org/01j8e0j24","country_code":"US","type":"education","lineage":["https://openalex.org/I226560621"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoyu Zhang","raw_affiliation_strings":["Computer Science Department, California State University, San Marcos, CA, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science Department, California State University, San Marcos, CA, USA","institution_ids":["https://openalex.org/I226560621"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046963673","display_name":"Vivek K. Jalahalli","orcid":null},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vivek K. Jalahalli","raw_affiliation_strings":["Electrical and Computer Engineering Department, San Diego State University, San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Department, San Diego State University, San Diego, CA, USA","institution_ids":["https://openalex.org/I26538001"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5101959878"],"corresponding_institution_ids":["https://openalex.org/I26538001"],"apc_list":null,"apc_paid":null,"fwci":0.1695,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.5336386,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":null,"first_page":"151","last_page":"158"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9990000128746033,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9990000128746033,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9987999796867371,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protease","display_name":"Protease","score":0.7305221557617188},{"id":"https://openalex.org/keywords/hiv-1-protease","display_name":"HIV-1 protease","score":0.6932077407836914},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.5683451294898987},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.564395546913147},{"id":"https://openalex.org/keywords/shape-analysis","display_name":"Shape analysis (program analysis)","score":0.4749186933040619},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4644508361816406},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.44663190841674805},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4417588412761688},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.42544203996658325},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3544767200946808},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33969199657440186},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25520968437194824},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1561814546585083},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.13902905583381653},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13596069812774658},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.1174885630607605},{"id":"https://openalex.org/keywords/static-analysis","display_name":"Static analysis","score":0.08633413910865784},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08002817630767822}],"concepts":[{"id":"https://openalex.org/C2776714187","wikidata":"https://www.wikidata.org/wiki/Q212410","display_name":"Protease","level":3,"score":0.7305221557617188},{"id":"https://openalex.org/C2777583353","wikidata":"https://www.wikidata.org/wiki/Q410261","display_name":"HIV-1 protease","level":4,"score":0.6932077407836914},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.5683451294898987},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.564395546913147},{"id":"https://openalex.org/C112604564","wikidata":"https://www.wikidata.org/wiki/Q7489226","display_name":"Shape analysis (program analysis)","level":3,"score":0.4749186933040619},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4644508361816406},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.44663190841674805},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4417588412761688},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.42544203996658325},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3544767200946808},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33969199657440186},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25520968437194824},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1561814546585083},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.13902905583381653},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13596069812774658},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.1174885630607605},{"id":"https://openalex.org/C97686452","wikidata":"https://www.wikidata.org/wiki/Q7604153","display_name":"Static analysis","level":2,"score":0.08633413910865784},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08002817630767822},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2008.4675772","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2008.4675772","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8199999928474426,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W195327248","https://openalex.org/W1501500081","https://openalex.org/W1517566065","https://openalex.org/W1978184203","https://openalex.org/W1983304433","https://openalex.org/W1984563996","https://openalex.org/W1984591534","https://openalex.org/W1986853728","https://openalex.org/W1999353322","https://openalex.org/W2009570821","https://openalex.org/W2019951137","https://openalex.org/W2020652215","https://openalex.org/W2027853992","https://openalex.org/W2029582401","https://openalex.org/W2031194866","https://openalex.org/W2032166713","https://openalex.org/W2049981393","https://openalex.org/W2053939793","https://openalex.org/W2058463742","https://openalex.org/W2081702044","https://openalex.org/W2085753639","https://openalex.org/W2086501194","https://openalex.org/W2091563009","https://openalex.org/W2098871350","https://openalex.org/W2103794058","https://openalex.org/W2105902442","https://openalex.org/W2112878061","https://openalex.org/W2112946416","https://openalex.org/W2128402268","https://openalex.org/W2130479394","https://openalex.org/W2134601920","https://openalex.org/W2137382111","https://openalex.org/W2139942857","https://openalex.org/W2144071905","https://openalex.org/W2144714500","https://openalex.org/W2151345203","https://openalex.org/W2159498975","https://openalex.org/W2162196815","https://openalex.org/W2289301985","https://openalex.org/W2312729996","https://openalex.org/W4245668478","https://openalex.org/W6607895961","https://openalex.org/W6629971530","https://openalex.org/W6696248736"],"related_works":["https://openalex.org/W2049250591","https://openalex.org/W2126525653","https://openalex.org/W2801493643","https://openalex.org/W2256372280","https://openalex.org/W4245621070","https://openalex.org/W2075748968","https://openalex.org/W1516237426","https://openalex.org/W2128025541","https://openalex.org/W1986563007","https://openalex.org/W1969009510"],"abstract_inverted_index":{"Using":[0],"a":[1,5,40],"shape":[2,22,53,85],"analysis":[3,68],"technique,":[4],"dataset":[6],"of":[7,39,42,79,87,91],"83":[8],"(20":[9],"wild-type":[10],"and":[11,37,46,55],"63":[12],"mutated)":[13],"HIV-1":[14],"protease":[15],"crystal":[16],"structures":[17,29],"is":[18],"analyzed":[19],"for":[20],"the":[21,51,77,84,88],"changes":[23],"in":[24],"their":[25],"binding":[26,89],"pockets.":[27],"The":[28],"were":[30,64],"reported":[31],"with":[32],"different":[33],"bound":[34],"inhibitors":[35],"(ligands)":[36],"consist":[38],"variety":[41],"mutations.":[43],"Several":[44],"geometrical":[45],"topological":[47],"attributes":[48,74],"based":[49],"on":[50,83],"volumetric":[52],"function":[54,63],"few":[56],"other":[57],"additional":[58],"properties":[59],"like":[60],"electrostatic":[61],"potential":[62],"calculated.":[65],"A":[66],"cluster":[67],"was":[69],"performed":[70],"using":[71],"these":[72],"calculated":[73],"to":[75],"investigate":[76],"effect":[78],"mutations":[80],"or":[81],"ligand":[82],"change":[86],"pocket":[90],"HIV":[92],"protease.":[93]},"counts_by_year":[{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
