{"id":"https://openalex.org/W2083221543","doi":"https://doi.org/10.1007/s10822-010-9397-6","title":"Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes","display_name":"Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes","publication_year":2010,"publication_date":"2010-11-03","ids":{"openalex":"https://openalex.org/W2083221543","doi":"https://doi.org/10.1007/s10822-010-9397-6","mag":"2083221543","pmid":"https://pubmed.ncbi.nlm.nih.gov/21053051"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-010-9397-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-010-9397-6","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","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/A5066959335","display_name":"Alpeshkumar K. Malde","orcid":"https://orcid.org/0000-0002-8181-1619"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Alpeshkumar K. Malde","raw_affiliation_strings":["School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, 4072, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060550957","display_name":"Alan E. Mark","orcid":"https://orcid.org/0000-0001-5880-4798"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Alan E. Mark","raw_affiliation_strings":["Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia","School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, 4072, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, 4072, Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5060550957"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":2.3829,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.89328164,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"1","first_page":"1","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9991999864578247,"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":0.9991999864578247,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9988999962806702,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9986000061035156,"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/ligand","display_name":"Ligand (biochemistry)","score":0.6679787635803223},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.6136773228645325},{"id":"https://openalex.org/keywords/tautomer","display_name":"Tautomer","score":0.6019384264945984},{"id":"https://openalex.org/keywords/protonation","display_name":"Protonation","score":0.5744152665138245},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5656343102455139},{"id":"https://openalex.org/keywords/diffraction","display_name":"Diffraction","score":0.553300678730011},{"id":"https://openalex.org/keywords/electrostatics","display_name":"Electrostatics","score":0.5186021327972412},{"id":"https://openalex.org/keywords/resolution","display_name":"Resolution (logic)","score":0.47523096203804016},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.4738785922527313},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4703298509120941},{"id":"https://openalex.org/keywords/x-ray-crystallography","display_name":"X-ray crystallography","score":0.46188870072364807},{"id":"https://openalex.org/keywords/crystal-structure","display_name":"Crystal structure","score":0.45478901267051697},{"id":"https://openalex.org/keywords/drug-design","display_name":"Drug design","score":0.4538669288158417},{"id":"https://openalex.org/keywords/orientation","display_name":"Orientation (vector space)","score":0.43559765815734863},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3647145926952362},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.34454745054244995},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.2611376941204071},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16870054602622986},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.13031312823295593},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.124269038438797},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.1128905713558197}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6679787635803223},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.6136773228645325},{"id":"https://openalex.org/C111233374","wikidata":"https://www.wikidata.org/wiki/Q334640","display_name":"Tautomer","level":2,"score":0.6019384264945984},{"id":"https://openalex.org/C30095370","wikidata":"https://www.wikidata.org/wiki/Q899488","display_name":"Protonation","level":3,"score":0.5744152665138245},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5656343102455139},{"id":"https://openalex.org/C207114421","wikidata":"https://www.wikidata.org/wiki/Q133900","display_name":"Diffraction","level":2,"score":0.553300678730011},{"id":"https://openalex.org/C117626034","wikidata":"https://www.wikidata.org/wiki/Q26336","display_name":"Electrostatics","level":2,"score":0.5186021327972412},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.47523096203804016},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.4738785922527313},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4703298509120941},{"id":"https://openalex.org/C50515024","wikidata":"https://www.wikidata.org/wiki/Q826582","display_name":"X-ray crystallography","level":3,"score":0.46188870072364807},{"id":"https://openalex.org/C115624301","wikidata":"https://www.wikidata.org/wiki/Q895901","display_name":"Crystal structure","level":2,"score":0.45478901267051697},{"id":"https://openalex.org/C192071366","wikidata":"https://www.wikidata.org/wiki/Q2991682","display_name":"Drug design","level":2,"score":0.4538669288158417},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.43559765815734863},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3647145926952362},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.34454745054244995},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.2611376941204071},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16870054602622986},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.13031312823295593},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.124269038438797},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.1128905713558197},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"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":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-010-9397-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-010-9397-6","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:21053051","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21053051","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 computer-aided molecular design","raw_type":null},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:231132","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1605578858","https://openalex.org/W1656114533","https://openalex.org/W1970410138","https://openalex.org/W1972280148","https://openalex.org/W1973244147","https://openalex.org/W1979563586","https://openalex.org/W1980937780","https://openalex.org/W1987453984","https://openalex.org/W1989749389","https://openalex.org/W1995952752","https://openalex.org/W2012748209","https://openalex.org/W2015688756","https://openalex.org/W2019701333","https://openalex.org/W2020983121","https://openalex.org/W2023242541","https://openalex.org/W2024745990","https://openalex.org/W2030850720","https://openalex.org/W2033129152","https://openalex.org/W2033957087","https://openalex.org/W2043116111","https://openalex.org/W2050226017","https://openalex.org/W2055989425","https://openalex.org/W2058159886","https://openalex.org/W2066405179","https://openalex.org/W2067484324","https://openalex.org/W2079769193","https://openalex.org/W2083965528","https://openalex.org/W2087894985","https://openalex.org/W2090143109","https://openalex.org/W2090338420","https://openalex.org/W2096196180","https://openalex.org/W2096849227","https://openalex.org/W2098834046","https://openalex.org/W2113578501","https://openalex.org/W2114367386","https://openalex.org/W2115339329","https://openalex.org/W2116275717","https://openalex.org/W2116426967","https://openalex.org/W2122339645","https://openalex.org/W2128332459","https://openalex.org/W2133096761","https://openalex.org/W2133555349","https://openalex.org/W2133773344","https://openalex.org/W2136530976","https://openalex.org/W2145355174","https://openalex.org/W2148694319","https://openalex.org/W2160276605"],"related_works":["https://openalex.org/W2105466274","https://openalex.org/W2010636594","https://openalex.org/W4283711622","https://openalex.org/W2000027971","https://openalex.org/W2049273629","https://openalex.org/W3002554271","https://openalex.org/W2914268038","https://openalex.org/W1993849124","https://openalex.org/W2417721574","https://openalex.org/W1969904624"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":6}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}