{"id":"https://openalex.org/W2722005050","doi":"https://doi.org/10.1093/bib/bbx022","title":"Review and comparative assessment of sequence-based predictors of protein-binding residues","display_name":"Review and comparative assessment of sequence-based predictors of protein-binding residues","publication_year":2017,"publication_date":"2017-02-15","ids":{"openalex":"https://openalex.org/W2722005050","doi":"https://doi.org/10.1093/bib/bbx022","mag":"2722005050","pmid":"https://pubmed.ncbi.nlm.nih.gov/28334258"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbx022","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx022","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","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/A5057149168","display_name":"Jian Zhang","orcid":"https://orcid.org/0000-0001-7155-7760"},"institutions":[{"id":"https://openalex.org/I130750295","display_name":"Xinyang Normal University","ror":"https://ror.org/0190x2a66","country_code":"CN","type":"education","lineage":["https://openalex.org/I130750295"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Zhang","raw_affiliation_strings":["School of Computer and Information Technology, Xinyang Normal University"],"affiliations":[{"raw_affiliation_string":"School of Computer and Information Technology, Xinyang Normal University","institution_ids":["https://openalex.org/I130750295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088423732","display_name":"Lukasz Kurgan","orcid":"https://orcid.org/0000-0002-7749-0314"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lukasz Kurgan","raw_affiliation_strings":["Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA","institution_ids":["https://openalex.org/I184840846"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5088423732"],"corresponding_institution_ids":["https://openalex.org/I184840846"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.8279,"has_fulltext":false,"cited_by_count":122,"citation_normalized_percentile":{"value":0.94486799,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"19","issue":"5","first_page":"821","last_page":"837"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9979000091552734,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9939000010490417,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5523371696472168},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.42801135778427124},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4191684126853943},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.41817939281463623},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38484373688697815},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3017624020576477},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27945101261138916},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2664846181869507}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5523371696472168},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.42801135778427124},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4191684126853943},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.41817939281463623},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38484373688697815},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3017624020576477},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27945101261138916},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2664846181869507},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbx022","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbx022","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28334258","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28334258","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.75,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":98,"referenced_works":["https://openalex.org/W1030883578","https://openalex.org/W1534302414","https://openalex.org/W1815147785","https://openalex.org/W1829437510","https://openalex.org/W1886978693","https://openalex.org/W1901968134","https://openalex.org/W1963886906","https://openalex.org/W1964084224","https://openalex.org/W1964880253","https://openalex.org/W1965150339","https://openalex.org/W1968278549","https://openalex.org/W1969156759","https://openalex.org/W1974987674","https://openalex.org/W1978987398","https://openalex.org/W1979284950","https://openalex.org/W1982267716","https://openalex.org/W1985919127","https://openalex.org/W1988972583","https://openalex.org/W1989949705","https://openalex.org/W1990740967","https://openalex.org/W1993856052","https://openalex.org/W2009672036","https://openalex.org/W2009768397","https://openalex.org/W2013503778","https://openalex.org/W2015802360","https://openalex.org/W2017230497","https://openalex.org/W2018661561","https://openalex.org/W2021041804","https://openalex.org/W2029964710","https://openalex.org/W2031198583","https://openalex.org/W2043272237","https://openalex.org/W2043638247","https://openalex.org/W2044955175","https://openalex.org/W2046407284","https://openalex.org/W2056169996","https://openalex.org/W2056335234","https://openalex.org/W2070871842","https://openalex.org/W2074019887","https://openalex.org/W2074104861","https://openalex.org/W2078999665","https://openalex.org/W2080167197","https://openalex.org/W2085809045","https://openalex.org/W2087322782","https://openalex.org/W2091411809","https://openalex.org/W2092123736","https://openalex.org/W2103485392","https://openalex.org/W2108134720","https://openalex.org/W2109300715","https://openalex.org/W2110705561","https://openalex.org/W2118737745","https://openalex.org/W2120770540","https://openalex.org/W2124959034","https://openalex.org/W2125950230","https://openalex.org/W2130479394","https://openalex.org/W2130754579","https://openalex.org/W2131275135","https://openalex.org/W2139212933","https://openalex.org/W2139373949","https://openalex.org/W2141627824","https://openalex.org/W2142529984","https://openalex.org/W2144811782","https://openalex.org/W2145023212","https://openalex.org/W2151412657","https://openalex.org/W2152521138","https://openalex.org/W2152705149","https://openalex.org/W2155006702","https://openalex.org/W2155194485","https://openalex.org/W2156215828","https://openalex.org/W2157163921","https://openalex.org/W2158714788","https://openalex.org/W2161701113","https://openalex.org/W2161922860","https://openalex.org/W2162259397","https://openalex.org/W2162392441","https://openalex.org/W2163879391","https://openalex.org/W2183771695","https://openalex.org/W2192578595","https://openalex.org/W2211863317","https://openalex.org/W2223549968","https://openalex.org/W2242104984","https://openalex.org/W2264362083","https://openalex.org/W2270702445","https://openalex.org/W2280888683","https://openalex.org/W2283929195","https://openalex.org/W2321247274","https://openalex.org/W2340589369","https://openalex.org/W2342374505","https://openalex.org/W2344144945","https://openalex.org/W2396940995","https://openalex.org/W2413107225","https://openalex.org/W2414776391","https://openalex.org/W2420922808","https://openalex.org/W2461928526","https://openalex.org/W2491115272","https://openalex.org/W2739999456","https://openalex.org/W2911964244","https://openalex.org/W4238372608","https://openalex.org/W6696048330"],"related_works":["https://openalex.org/W2099982459","https://openalex.org/W1982038138","https://openalex.org/W1974422922","https://openalex.org/W3187431608","https://openalex.org/W2109298101","https://openalex.org/W4309353019","https://openalex.org/W2914490533","https://openalex.org/W2007507741","https://openalex.org/W2159860826","https://openalex.org/W2133294187"],"abstract_inverted_index":{"Understanding":[0],"of":[1,11,20,50,105,108,169,216,224,228,237,239],"molecular":[2],"mechanisms":[3],"that":[4,31,40,67,72,121,132,147],"govern":[5],"protein-protein":[6,12,33],"interactions":[7,34],"and":[8,18,23,53,71,86,88,96,114,128,131,155,171,183,201,220,234],"accurate":[9,16,218],"modeling":[10],"docking":[13],"rely":[14],"on":[15,63],"identification":[17],"prediction":[19,168],"protein-binding":[21,24,45,54,109,127,160,193],"partners":[22],"residues.":[25,161,194],"We":[26,61,81,98,119,195],"review":[27],"over":[28],"40":[29],"methods":[30,39,66,134,140,182],"predict":[32,41],"from":[35,158],"protein":[36,43,59,79,175],"sequences":[37,52],"including":[38],"interacting":[42,51],"pairs,":[44],"residues":[46,55,110,130,146,173],"for":[47,179,198,212],"a":[48,57,112,213,225],"pair":[49],"in":[56,231],"single":[58],"chain.":[60],"focus":[62],"the":[64,122,159,166,188,191,210,229,240],"latter":[65],"provide":[68],"residue-level":[69],"annotations":[70],"can":[73],"be":[74],"broadly":[75],"applied":[76],"to":[77,93,143,190],"all":[78,180],"sequences.":[80],"compare":[82],"their":[83,94],"architectures,":[84],"inputs":[85],"outputs,":[87],"we":[89,202,208],"discuss":[90,196],"aspects":[91],"related":[92],"assessment":[95,227],"availability.":[97],"also":[99],"perform":[100],"first-of-its-kind":[101],"comprehensive":[102,226],"empirical":[103],"comparison":[104],"representative":[106],"predictors":[107,124,219],"using":[111],"novel":[113],"high-quality":[115],"benchmark":[116],"data":[117,221],"set.":[118],"show":[120],"selected":[123],"accurately":[125,144],"discriminate":[126],"non-binding":[129],"newer":[133],"outperform":[135],"older":[136],"designs.":[137],"However,":[138],"these":[139],"are":[141],"unable":[142],"separate":[145],"bind":[148],"other":[149],"molecules,":[150],"such":[151],"as":[152,165,174],"DNA,":[153],"RNA":[154],"small":[156],"ligands,":[157],"This":[162],"cross-prediction,":[163],"defined":[164],"incorrect":[167],"nucleic-acid-":[170],"small-ligand-binding":[172],"binding,":[176],"is":[177,184],"substantial":[178],"evaluated":[181],"not":[185],"driven":[186],"by":[187],"proximity":[189],"native":[192],"reasons":[197],"this":[199],"drawback":[200],"offer":[203],"several":[204],"recommendations.":[205],"In":[206],"particular,":[207],"postulate":[209],"need":[211],"new":[214],"generation":[215],"more":[217],"sets,":[222],"inclusion":[223],"cross-predictions":[230],"future":[232],"studies":[233],"higher":[235],"standards":[236],"availability":[238],"published":[241],"methods.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":22},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
