{"id":"https://openalex.org/W2001816314","doi":"https://doi.org/10.1007/s10822-008-9196-5","title":"Recommendations for evaluation of computational methods","display_name":"Recommendations for evaluation of computational methods","publication_year":2008,"publication_date":"2008-03-01","ids":{"openalex":"https://openalex.org/W2001816314","doi":"https://doi.org/10.1007/s10822-008-9196-5","mag":"2001816314","pmid":"https://pubmed.ncbi.nlm.nih.gov/18338228"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-008-9196-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-008-9196-5","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-008-9196-5.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10822-008-9196-5.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005430934","display_name":"Ajay N. Jain","orcid":"https://orcid.org/0000-0003-4641-8501"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ajay N. Jain","raw_affiliation_strings":["University of California San Francisco, Box 0128, San Francisco, CA 94143-0128, USA. ajain@jainlab.org","University of California, San Francisco, Box 0128, San Francisco, CA 94143-0128, USA"],"affiliations":[{"raw_affiliation_string":"University of California San Francisco, Box 0128, San Francisco, CA 94143-0128, USA. ajain@jainlab.org","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"University of California, San Francisco, Box 0128, San Francisco, CA 94143-0128, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102879646","display_name":"Anthony Nicholls","orcid":"https://orcid.org/0000-0001-8488-9641"},"institutions":[{"id":"https://openalex.org/I4210106217","display_name":"OpenEye (Sweden)","ror":"https://ror.org/019r2ty74","country_code":"SE","type":"company","lineage":["https://openalex.org/I4210106217"]},{"id":"https://openalex.org/I4210158493","display_name":"Open Source Science Project","ror":"https://ror.org/0523sbv14","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210158493"]}],"countries":["SE","US"],"is_corresponding":false,"raw_author_name":"Anthony Nicholls","raw_affiliation_strings":["OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM, 87508, USA","OpenEye Scientific Software"],"affiliations":[{"raw_affiliation_string":"OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM, 87508, USA","institution_ids":["https://openalex.org/I4210158493"]},{"raw_affiliation_string":"OpenEye Scientific Software","institution_ids":["https://openalex.org/I4210106217"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5005430934"],"corresponding_institution_ids":["https://openalex.org/I180670191"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":{"value":2890,"currency":"EUR","value_usd":3690},"fwci":28.8114,"has_fulltext":true,"cited_by_count":349,"citation_normalized_percentile":{"value":0.99811162,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"22","issue":"3-4","first_page":"133","last_page":"139"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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/T11235","display_name":"Statistical Methods in Clinical Trials","score":0.9925000071525574,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.9876999855041504,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7367963790893555},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7039002180099487},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.6479901075363159},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6098775267601013},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4894634485244751},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.4255709648132324},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.41100192070007324},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39918339252471924},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.2873116433620453},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12168702483177185},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.11667436361312866}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7367963790893555},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7039002180099487},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.6479901075363159},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6098775267601013},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4894634485244751},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.4255709648132324},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.41100192070007324},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39918339252471924},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2873116433620453},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12168702483177185},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.11667436361312866},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005069","descriptor_name":"Evaluation Studies as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-008-9196-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-008-9196-5","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-008-9196-5.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:18338228","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18338228","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:pubmedcentral.nih.gov:2311385","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2311385","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Aided Mol Des","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s10822-008-9196-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-008-9196-5","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-008-9196-5.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","score":0.6399999856948853,"display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2001816314.pdf","grobid_xml":"https://content.openalex.org/works/W2001816314.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1970208561","https://openalex.org/W1988859391","https://openalex.org/W2013291622","https://openalex.org/W2015080758","https://openalex.org/W2015907087","https://openalex.org/W2034553680","https://openalex.org/W2039197391","https://openalex.org/W2039526577","https://openalex.org/W2058433776","https://openalex.org/W2058820833","https://openalex.org/W2081266727","https://openalex.org/W2085789404","https://openalex.org/W2115318272","https://openalex.org/W2809555287"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W972276598","https://openalex.org/W2087343574","https://openalex.org/W4246352526","https://openalex.org/W4249571711"],"abstract_inverted_index":{"The":[0],"field":[1,60],"of":[2,17,21,36,53,64,71,91],"computational":[3],"chemistry,":[4],"particularly":[5],"as":[6],"applied":[7],"to":[8,24,39,68,84],"drug":[9],"design,":[10],"has":[11],"become":[12],"increasingly":[13],"important":[14],"in":[15,93],"terms":[16],"the":[18,59],"practical":[19,101],"application":[20],"predictive":[22],"modeling":[23],"pharmaceutical":[25],"research":[26],"and":[27,51,76,120,126],"development.":[28],"Tools":[29],"for":[30,46,100,111,117,123],"exploiting":[31],"protein":[32],"structures":[33],"or":[34,88],"sets":[35],"ligands":[37],"known":[38],"bind":[40],"particular":[41],"targets":[42],"can":[43],"be":[44,83],"used":[45],"binding-mode":[47],"prediction,":[48],"virtual":[49],"screening,":[50],"prediction":[52],"activity.":[54],"A":[55],"serious":[56],"weakness":[57],"within":[58],"is":[61],"a":[62,94,106],"lack":[63],"standards":[65],"with":[66,109],"respect":[67],"quantitative":[69],"evaluation":[70],"methods,":[72],"data":[73,77,118],"set":[74,78],"preparation,":[75],"sharing.":[79],"Our":[80],"goal":[81],"should":[82],"report":[85],"new":[86],"methods":[87,92],"comparative":[89],"evaluations":[90],"manner":[95],"that":[96],"supports":[97],"decision":[98],"making":[99],"applications.":[102],"Here":[103],"we":[104],"propose":[105],"modest":[107],"beginning,":[108],"recommendations":[110],"requirements":[112,116],"on":[113],"statistical":[114],"reporting,":[115],"sharing,":[119],"best":[121],"practices":[122],"benchmark":[124],"preparation":[125],"usage.":[127]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":34},{"year":2021,"cited_by_count":30},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":19},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":18},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":16},{"year":2012,"cited_by_count":26}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
