{"id":"https://openalex.org/W1979552507","doi":"https://doi.org/10.1021/ci8003495","title":"Molecular Insights into 14-Membered Macrolides Using the MM-PBSA Method","display_name":"Molecular Insights into 14-Membered Macrolides Using the MM-PBSA Method","publication_year":2009,"publication_date":"2009-05-26","ids":{"openalex":"https://openalex.org/W1979552507","doi":"https://doi.org/10.1021/ci8003495","mag":"1979552507","pmid":"https://pubmed.ncbi.nlm.nih.gov/19469526"},"language":"en","primary_location":{"id":"doi:10.1021/ci8003495","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci8003495","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/A5062175281","display_name":"Wai Keat Yam","orcid":"https://orcid.org/0000-0003-4595-2796"},"institutions":[{"id":"https://openalex.org/I139322472","display_name":"Universiti Sains Malaysia","ror":"https://ror.org/02rgb2k63","country_code":"MY","type":"education","lineage":["https://openalex.org/I139322472"]},{"id":"https://openalex.org/I134138859","display_name":"Ministry of Science, Technology and Innovation","ror":"https://ror.org/012s3r374","country_code":"MY","type":"government","lineage":["https://openalex.org/I134138859"]}],"countries":["MY"],"is_corresponding":true,"raw_author_name":"Wai Keat Yam","raw_affiliation_strings":["Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia, and Division for Advanced Drug Delivery, Malaysian Institute of Pharmaceuticals and Nutraceuticals, Malaysian Ministry of Science, Technology and Innovation, SAINS@USM 10, Persiaran Bukit Jambul, 11900 Bukit Jambul, Pulau Pinang, Malaysia"],"affiliations":[{"raw_affiliation_string":"Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia, and Division for Advanced Drug Delivery, Malaysian Institute of Pharmaceuticals and Nutraceuticals, Malaysian Ministry of Science, Technology and Innovation, SAINS@USM 10, Persiaran Bukit Jambul, 11900 Bukit Jambul, Pulau Pinang, Malaysia","institution_ids":["https://openalex.org/I134138859","https://openalex.org/I139322472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008474034","display_name":"Habibah A. Wahab","orcid":"https://orcid.org/0000-0002-8353-8679"},"institutions":[{"id":"https://openalex.org/I139322472","display_name":"Universiti Sains Malaysia","ror":"https://ror.org/02rgb2k63","country_code":"MY","type":"education","lineage":["https://openalex.org/I139322472"]},{"id":"https://openalex.org/I134138859","display_name":"Ministry of Science, Technology and Innovation","ror":"https://ror.org/012s3r374","country_code":"MY","type":"government","lineage":["https://openalex.org/I134138859"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Habibah A. Wahab","raw_affiliation_strings":["Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia, and Division for Advanced Drug Delivery, Malaysian Institute of Pharmaceuticals and Nutraceuticals, Malaysian Ministry of Science, Technology and Innovation, SAINS@USM 10, Persiaran Bukit Jambul, 11900 Bukit Jambul, Pulau Pinang, Malaysia"],"affiliations":[{"raw_affiliation_string":"Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia, and Division for Advanced Drug Delivery, Malaysian Institute of Pharmaceuticals and Nutraceuticals, Malaysian Ministry of Science, Technology and Innovation, SAINS@USM 10, Persiaran Bukit Jambul, 11900 Bukit Jambul, Pulau Pinang, Malaysia","institution_ids":["https://openalex.org/I134138859","https://openalex.org/I139322472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5062175281"],"corresponding_institution_ids":["https://openalex.org/I134138859","https://openalex.org/I139322472"],"apc_list":null,"apc_paid":null,"fwci":0.7874,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.70007119,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"49","issue":"6","first_page":"1558","last_page":"1567"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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":0.9973999857902527,"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"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973000288009644,"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/chemistry","display_name":"Chemistry","score":0.44591641426086426},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36210790276527405},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.32327497005462646},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.270003080368042},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24123427271842957}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.44591641426086426},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36210790276527405},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.32327497005462646},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.270003080368042},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24123427271842957}],"mesh":[{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004917","descriptor_name":"Erythromycin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004917","descriptor_name":"Erythromycin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004917","descriptor_name":"Erythromycin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004917","descriptor_name":"Erythromycin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004917","descriptor_name":"Erythromycin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004917","descriptor_name":"Erythromycin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":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":"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":"D012996","descriptor_name":"Solutions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012996","descriptor_name":"Solutions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012996","descriptor_name":"Solutions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","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":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015575","descriptor_name":"Roxithromycin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015575","descriptor_name":"Roxithromycin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015575","descriptor_name":"Roxithromycin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015575","descriptor_name":"Roxithromycin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015575","descriptor_name":"Roxithromycin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015575","descriptor_name":"Roxithromycin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018942","descriptor_name":"Macrolides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018942","descriptor_name":"Macrolides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018942","descriptor_name":"Macrolides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018942","descriptor_name":"Macrolides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018942","descriptor_name":"Macrolides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018942","descriptor_name":"Macrolides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054681","descriptor_name":"Ribosome Subunits, Large, Bacterial","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054681","descriptor_name":"Ribosome Subunits, Large, Bacterial","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054681","descriptor_name":"Ribosome Subunits, Large, Bacterial","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci8003495","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci8003495","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:19469526","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19469526","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":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8600000143051147}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W619279939","https://openalex.org/W1484216450","https://openalex.org/W1974413143","https://openalex.org/W1975580333","https://openalex.org/W1976499671","https://openalex.org/W1980674913","https://openalex.org/W1988705808","https://openalex.org/W1988808892","https://openalex.org/W1989823425","https://openalex.org/W2000911325","https://openalex.org/W2002649351","https://openalex.org/W2006475108","https://openalex.org/W2012443293","https://openalex.org/W2023563495","https://openalex.org/W2028521503","https://openalex.org/W2029667189","https://openalex.org/W2035266068","https://openalex.org/W2036619402","https://openalex.org/W2039026588","https://openalex.org/W2039062180","https://openalex.org/W2039833566","https://openalex.org/W2043158848","https://openalex.org/W2047275679","https://openalex.org/W2048214699","https://openalex.org/W2048619259","https://openalex.org/W2073673177","https://openalex.org/W2075369230","https://openalex.org/W2079285768","https://openalex.org/W2083164919","https://openalex.org/W2092250290","https://openalex.org/W2092443343","https://openalex.org/W2095398138","https://openalex.org/W2097732752","https://openalex.org/W2101114936","https://openalex.org/W2104500040","https://openalex.org/W2105289202","https://openalex.org/W2105838618","https://openalex.org/W2108304234","https://openalex.org/W2109574319","https://openalex.org/W2110562802","https://openalex.org/W2110655770","https://openalex.org/W2116696124","https://openalex.org/W2122199548","https://openalex.org/W2136096071","https://openalex.org/W2139721558","https://openalex.org/W2144190398","https://openalex.org/W2147993766","https://openalex.org/W2150112042","https://openalex.org/W2156917764","https://openalex.org/W2162627788","https://openalex.org/W2165600264","https://openalex.org/W2166117980","https://openalex.org/W2166234471","https://openalex.org/W2170958132","https://openalex.org/W2326410228"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"Erythromycin":[0],"A":[1],"and":[2,77,150,164,179,215],"roxithromycin":[3],"are":[4,176,198],"clinically":[5],"important":[6,178],"macrolide":[7,42,224],"antibiotics":[8],"that":[9,157],"selectively":[10],"act":[11],"on":[12],"the":[13,27,31,55,74,78,88,109,120,135,141,145,170,185,190,203,219],"bacterial":[14],"50S":[15],"large":[16],"ribosomal":[17],"subunit":[18],"to":[19,46,54,69,108,133,189,200,202],"inhibit":[20],"bacteria's":[21],"protein":[22],"elongation":[23],"process":[24],"by":[25],"blocking":[26],"exit":[28],"tunnel":[29],"for":[30,82,101,122],"nascent":[32],"peptide":[33],"away":[34],"from":[35,172,195],"ribosome.":[36],"The":[37,96,193],"detailed":[38,207],"molecular":[39,63,75,89],"mechanism":[40,208],"of":[41,126,137,148,187,205,209,221],"binding":[43,79,98,121,142,146,186,191],"is":[44,51],"yet":[45],"be":[47],"elucidated":[48],"as":[49],"it":[50],"currently":[52],"known":[53],"most":[56],"general":[57],"idea":[58],"only.":[59],"In":[60],"this":[61,196],"study,":[62],"dynamics":[64],"(MD)":[65],"simulation":[66],"was":[67,131],"employed":[68],"study":[70,197],"their":[71],"interaction":[72],"at":[73,140],"level,":[76],"free":[80,99],"energies":[81,100],"both":[83,102,123],"systems":[84,103],"were":[85,104,158],"calculated":[86,97],"using":[87],"mechanics":[90],"Poisson-Boltzmann":[91],"surface":[92],"area":[93],"(MM-PBSA)":[94],"method.":[95],"slightly":[105],"overestimated":[106],"compared":[107],"experimental":[110,163],"values,":[111],"but":[112],"individual":[113],"energy":[114],"terms":[115],"enabled":[116],"better":[117],"understanding":[118,204],"in":[119,159,184,211,218],"systems.":[124],"Decomposition":[125],"results":[127],"into":[128],"residue":[129,139],"basis":[130],"able":[132],"show":[134],"contribution":[136,183],"each":[138],"pocket":[143],"toward":[144],"affinity":[147],"macrolides":[149,188],"hence":[151],"identified":[152],"several":[153],"key":[154],"interacting":[155],"residues":[156],"agreement":[160],"with":[161],"previous":[162],"computational":[165],"data.":[166],"Results":[167],"also":[168],"indicated":[169],"contributions":[171],"van":[173],"der":[174],"Waals":[175],"more":[177],"significant":[180],"than":[181],"electrostatic":[182],"pocket.":[192],"findings":[194],"expected":[199],"contribute":[201],"a":[206,212,222],"action":[210],"quantitative":[213],"matter":[214],"thus":[216],"assisting":[217],"development":[220],"safer":[223],"antibiotic.":[225]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}