{"id":"https://openalex.org/W4280651636","doi":"https://doi.org/10.1109/tcbb.2022.3173437","title":"SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features","display_name":"SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features","publication_year":2022,"publication_date":"2022-05-10","ids":{"openalex":"https://openalex.org/W4280651636","doi":"https://doi.org/10.1109/tcbb.2022.3173437","pmid":"https://pubmed.ncbi.nlm.nih.gov/35536812"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3173437","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3173437","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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/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, Xinyang, Henan, China"],"raw_orcid":"https://orcid.org/0000-0001-7155-7760","affiliations":[{"raw_affiliation_string":"School of Computer and Information Technology, Xinyang Normal University, Xinyang, Henan, China","institution_ids":["https://openalex.org/I130750295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064754725","display_name":"Feng Zhou","orcid":"https://orcid.org/0000-0001-9231-3538"},"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":"Feng Zhou","raw_affiliation_strings":["School of Computer and Information Technology, Xinyang Normal University, Xinyang, Henan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Information Technology, Xinyang Normal University, Xinyang, Henan, China","institution_ids":["https://openalex.org/I130750295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048224150","display_name":"Xingchen Liang","orcid":null},"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":"Xingchen Liang","raw_affiliation_strings":["School of Computer and Information Technology, Xinyang Normal University, Xinyang, Henan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Information Technology, Xinyang Normal University, Xinyang, Henan, China","institution_ids":["https://openalex.org/I130750295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101577184","display_name":"Guifu Yang","orcid":"https://orcid.org/0000-0003-3284-0584"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guifu Yang","raw_affiliation_strings":["School of Information Science and Technology, Northeast Normal University, Changchun, Jilin, China"],"raw_orcid":"https://orcid.org/0000-0003-3284-0584","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University, Changchun, Jilin, China","institution_ids":["https://openalex.org/I184983240"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.7184,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.72265336,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":"20","issue":"2","first_page":"1406","last_page":"1416"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"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":0.9995999932289124,"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/T12254","display_name":"Machine Learning in Bioinformatics","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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9962999820709229,"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/sequence","display_name":"Sequence (biology)","score":0.6935907006263733},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5507467985153198},{"id":"https://openalex.org/keywords/calcium","display_name":"Calcium","score":0.4405524730682373},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.353799432516098},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33145713806152344},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2713303565979004},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2556026875972748},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2176835834980011}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6935907006263733},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5507467985153198},{"id":"https://openalex.org/C519063684","wikidata":"https://www.wikidata.org/wiki/Q706","display_name":"Calcium","level":2,"score":0.4405524730682373},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.353799432516098},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33145713806152344},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2713303565979004},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2556026875972748},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2176835834980011},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002118","descriptor_name":"Calcium","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":"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":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2022.3173437","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3173437","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35536812","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35536812","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1261969788","display_name":null,"funder_award_id":"61802329","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320327564","display_name":"Xinyang Normal University","ror":"https://ror.org/0190x2a66"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W1605498756","https://openalex.org/W1924290394","https://openalex.org/W1963886906","https://openalex.org/W1973429805","https://openalex.org/W1983259744","https://openalex.org/W1987134040","https://openalex.org/W2009815491","https://openalex.org/W2009954700","https://openalex.org/W2011698799","https://openalex.org/W2013582153","https://openalex.org/W2018661561","https://openalex.org/W2019083595","https://openalex.org/W2027387590","https://openalex.org/W2029469631","https://openalex.org/W2043338013","https://openalex.org/W2043638247","https://openalex.org/W2045324102","https://openalex.org/W2051210555","https://openalex.org/W2052791761","https://openalex.org/W2062515707","https://openalex.org/W2062692445","https://openalex.org/W2065694935","https://openalex.org/W2072263349","https://openalex.org/W2076052898","https://openalex.org/W2085224242","https://openalex.org/W2087432921","https://openalex.org/W2089424629","https://openalex.org/W2089939121","https://openalex.org/W2092146175","https://openalex.org/W2097246321","https://openalex.org/W2098425296","https://openalex.org/W2098949725","https://openalex.org/W2099666638","https://openalex.org/W2101840868","https://openalex.org/W2102509567","https://openalex.org/W2103647733","https://openalex.org/W2104812418","https://openalex.org/W2107696205","https://openalex.org/W2114970874","https://openalex.org/W2137317896","https://openalex.org/W2140422012","https://openalex.org/W2146103350","https://openalex.org/W2157656310","https://openalex.org/W2158197581","https://openalex.org/W2167362634","https://openalex.org/W2170463736","https://openalex.org/W2200606379","https://openalex.org/W2259381440","https://openalex.org/W2325211585","https://openalex.org/W2401791034","https://openalex.org/W2465768314","https://openalex.org/W2472103865","https://openalex.org/W2527503499","https://openalex.org/W2528730608","https://openalex.org/W2554651637","https://openalex.org/W2620998958","https://openalex.org/W2722005050","https://openalex.org/W2751942010","https://openalex.org/W2766788471","https://openalex.org/W2767813457","https://openalex.org/W2800057751","https://openalex.org/W2806884808","https://openalex.org/W2934420151","https://openalex.org/W2941112903","https://openalex.org/W2950797462","https://openalex.org/W2955690154","https://openalex.org/W2990453062","https://openalex.org/W2995420950","https://openalex.org/W3136918052","https://openalex.org/W3196030482","https://openalex.org/W3205092939","https://openalex.org/W4220980683","https://openalex.org/W4233698560","https://openalex.org/W6640246690"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W1499732058","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2048213734","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W1989673413"],"abstract_inverted_index":{"Understanding":[0],"molecular":[1],"mechanisms":[2],"involved":[3],"in":[4],"calcium-protein":[5],"interactions":[6],"and":[7,58,79,95,103,164,178,192],"modeling":[8],"corresponding":[9],"docking":[10],"rely":[11],"on":[12,124,159],"the":[13,28,77,131,160,166,182,189,194],"accurate":[14,78],"identification":[15],"of":[16,22,30,52,82,144,150,184],"calcium-binding":[17,36,170],"residues":[18,46],"(CaBRs).":[19],"The":[20,173],"defects":[21],"experimentally":[23],"annotating":[24],"protein":[25],"functions":[26],"enhances":[27],"development":[29],"computational":[31],"approaches":[32],"that":[33,41,47,130],"correctly":[34],"identify":[35],"interactions.":[37],"Studies":[38],"have":[39],"reported":[40],"current":[42],"methods":[43],"severely":[44],"cross-predict":[45],"interact":[48],"with":[49,91],"other":[50],"types":[51,149],"molecules":[53],"(e.g.,":[54],"nucleic":[55,100],"acids,":[56],"proteins,":[57],"small":[59,104],"ligands)":[60],"as":[61,117,119],"CaBRs.":[62,83],"In":[63],"this":[64],"study,":[65],"a":[66,109],"novel":[67,110],"predictor":[68],"named":[69],"SCAMPER":[70,84,138],"(Selective":[71],"CAlciuM-binding":[72],"PrEdictoR)":[73],"is":[74,85,139],"proposed":[75,132,190],"for":[76],"specific":[80],"prediction":[81],"designed":[86,111],"using":[87],"newly":[88],"compiled":[89],"dataset":[90,128],"complete":[92],"UniProt":[93],"sequences":[94],"annotations,":[96],"which":[97],"include":[98],"calcium-binding,":[99],"acid-binding,":[101],"protein-binding,":[102],"ligand-binding":[105],"residues.":[106,153],"We":[107,154,187],"use":[108,165],"two-layer":[112],"scheme":[113],"to":[114,141,168],"perform":[115,156],"predictions":[116,158],"well":[118],"penalize":[120],"cross-predictions.":[121],"Empirical":[122],"tests":[123],"an":[125],"independent":[126],"test":[127],"reveals":[129],"method":[133,191],"significantly":[134],"outperforms":[135],"state-of-the-art":[136],"predictors.":[137],"proved":[140],"be":[142],"capable":[143],"distinguishing":[145],"CaBRs":[146,157],"from":[147],"different":[148],"metal-ion":[151],"binding":[152],"further":[155],"whole":[161],"human":[162],"proteome,":[163],"results":[167],"hypothesize":[169],"proteins":[171],"(CaBPs).":[172],"latest":[174],"experimental":[175],"verified":[176],"CaBPs":[177],"GO":[179],"analysis":[180],"prove":[181],"accuracy":[183],"our":[185],"predictions.":[186],"implement":[188],"share":[193],"data":[195],"at":[196],"http://www.inforstation.com/webservers/SCAMPER/.":[197]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}