{"id":"https://openalex.org/W2396663079","doi":"https://doi.org/10.1021/ci100350u","title":"LigBuilder 2: A Practical <i>de Novo</i> Drug Design Approach","display_name":"LigBuilder 2: A Practical <i>de Novo</i> Drug Design Approach","publication_year":2011,"publication_date":"2011-04-22","ids":{"openalex":"https://openalex.org/W2396663079","doi":"https://doi.org/10.1021/ci100350u","mag":"2396663079","pmid":"https://pubmed.ncbi.nlm.nih.gov/21513346"},"language":"en","primary_location":{"id":"doi:10.1021/ci100350u","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100350u","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/A5046581115","display_name":"Yaxia Yuan","orcid":"https://orcid.org/0000-0001-7094-4419"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaxia Yuan","raw_affiliation_strings":["BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","Center for Theoretical Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I4210116048","https://openalex.org/I20231570","https://openalex.org/I4391768210"]},{"raw_affiliation_string":"Center for Theoretical Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047704083","display_name":"Jianfeng Pei","orcid":"https://orcid.org/0000-0002-8482-1185"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianfeng Pei","raw_affiliation_strings":["Center for Theoretical Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Theoretical Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064049271","display_name":"Luhua Lai","orcid":"https://orcid.org/0000-0002-8343-7587"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Luhua Lai","raw_affiliation_strings":["BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","Center for Theoretical Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I4210116048","https://openalex.org/I20231570","https://openalex.org/I4391768210"]},{"raw_affiliation_string":"Center for Theoretical Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5047704083","https://openalex.org/A5064049271"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210116048","https://openalex.org/I4210160507","https://openalex.org/I4391768210"],"apc_list":null,"apc_paid":null,"fwci":10.7641,"has_fulltext":false,"cited_by_count":196,"citation_normalized_percentile":{"value":0.98901702,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"51","issue":"5","first_page":"1083","last_page":"1091"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991000294685364,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991000294685364,"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/T11845","display_name":"Cancer therapeutics and mechanisms","score":0.9958000183105469,"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/T13160","display_name":"Synthesis and Biological Evaluation","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/adme","display_name":"ADME","score":0.9434851408004761},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.6695593595504761},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5070273876190186},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.48982498049736023},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.48870065808296204},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4465904235839844},{"id":"https://openalex.org/keywords/distribution","display_name":"Distribution (mathematics)","score":0.4242251515388489},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3689364194869995},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.26527631282806396},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17432445287704468},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15033429861068726}],"concepts":[{"id":"https://openalex.org/C69366308","wikidata":"https://www.wikidata.org/wiki/Q2272286","display_name":"ADME","level":3,"score":0.9434851408004761},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.6695593595504761},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5070273876190186},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.48982498049736023},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.48870065808296204},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4465904235839844},{"id":"https://openalex.org/C110121322","wikidata":"https://www.wikidata.org/wiki/Q865811","display_name":"Distribution (mathematics)","level":2,"score":0.4242251515388489},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3689364194869995},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.26527631282806396},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17432445287704468},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15033429861068726},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000819","qualifier_name":"agonists","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000819","qualifier_name":"agonists","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000819","qualifier_name":"agonists","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci100350u","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100350u","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:21513346","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21513346","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/3","score":0.699999988079071,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1509196567","https://openalex.org/W1592238003","https://openalex.org/W1963654032","https://openalex.org/W1974346959","https://openalex.org/W1993046136","https://openalex.org/W1997388207","https://openalex.org/W1998723350","https://openalex.org/W2001851087","https://openalex.org/W2009299989","https://openalex.org/W2011230643","https://openalex.org/W2011647105","https://openalex.org/W2012197859","https://openalex.org/W2020503090","https://openalex.org/W2027465931","https://openalex.org/W2040617462","https://openalex.org/W2041686943","https://openalex.org/W2052907531","https://openalex.org/W2064535969","https://openalex.org/W2072227789","https://openalex.org/W2073627214","https://openalex.org/W2078048835","https://openalex.org/W2078521274","https://openalex.org/W2091563009","https://openalex.org/W2094661318","https://openalex.org/W2112109058","https://openalex.org/W2117996566","https://openalex.org/W2119099995","https://openalex.org/W2122161002","https://openalex.org/W2128402268","https://openalex.org/W2137658414","https://openalex.org/W2163188691","https://openalex.org/W2176516200","https://openalex.org/W2211224366"],"related_works":["https://openalex.org/W2088837113","https://openalex.org/W2158468919","https://openalex.org/W4244023852","https://openalex.org/W4308899116","https://openalex.org/W80237960","https://openalex.org/W1504949510","https://openalex.org/W2095641063","https://openalex.org/W3208474210","https://openalex.org/W1595741244","https://openalex.org/W180401638"],"abstract_inverted_index":{"We":[0],"have":[1],"developed":[2],"a":[3,28,48,67],"new":[4],"version":[5],"(2.0)":[6],"of":[7,21,40,47,69,86],"the":[8,18,36,41,45,63,81,84],"de":[9],"novo":[10],"drug":[11],"design":[12],"program":[13],"LigBuilder.":[14],"With":[15],"LigBuilder":[16],"2.0,":[17],"synthesis":[19],"accessibility":[20],"designed":[22,59],"compounds":[23],"can":[24],"be":[25],"analyzed,":[26],"and":[27,38,52,74,88,94,97],"cavity":[29],"detection":[30],"procedure":[31],"is":[32],"implemented":[33],"to":[34,53,60,79],"detect":[35],"positions":[37],"shapes":[39],"binding":[42],"sites":[43],"on":[44],"surface":[46],"given":[49],"protein":[50],"structure":[51],"quantitatively":[54],"estimate":[55],"drugability.":[56],"Ligands":[57],"are":[58,77],"best":[61],"fit":[62],"detected":[64],"cavities":[65],"using":[66],"set":[68],"rules":[70],"for":[71],"evaluation.":[72],"Drug-like":[73],"privileged":[75],"fragments":[76],"used":[78],"construct":[80],"ligands":[82],"with":[83],"aid":[85],"internal":[87],"external":[89],"absorption,":[90],"distribution,":[91],"metabolism,":[92],"excretion,":[93],"toxicity":[95],"(ADME/T)":[96],"drug-like":[98],"filters.":[99]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":22},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":8}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2016-06-24T00:00:00"}