{"id":"https://openalex.org/W2921356781","doi":"https://doi.org/10.1186/s12859-019-2627-6","title":"Predicting protein residue-residue contacts using random forests and deep networks","display_name":"Predicting protein residue-residue contacts using random forests and deep networks","publication_year":2019,"publication_date":"2019-03-01","ids":{"openalex":"https://openalex.org/W2921356781","doi":"https://doi.org/10.1186/s12859-019-2627-6","mag":"2921356781","pmid":"https://pubmed.ncbi.nlm.nih.gov/30871477"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2627-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2627-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2627-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2627-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011631125","display_name":"Joseph Luttrell","orcid":"https://orcid.org/0000-0001-5832-4487"},"institutions":[{"id":"https://openalex.org/I44854399","display_name":"University of Southern Mississippi","ror":"https://ror.org/0270vfa57","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I44854399"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joseph Luttrell","raw_affiliation_strings":["School of Computing Sciences and Computer Engineering, University of Southern Mississippi, 118 College Drive, Hattiesburg, MS, 39406, USA"],"affiliations":[{"raw_affiliation_string":"School of Computing Sciences and Computer Engineering, University of Southern Mississippi, 118 College Drive, Hattiesburg, MS, 39406, USA","institution_ids":["https://openalex.org/I44854399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392605","display_name":"Tong Liu","orcid":"https://orcid.org/0000-0001-5497-8117"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tong Liu","raw_affiliation_strings":["Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral Gables, FL, 33124, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral Gables, FL, 33124, USA","institution_ids":["https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100603445","display_name":"Chaoyang Zhang","orcid":"https://orcid.org/0000-0002-1221-0406"},"institutions":[{"id":"https://openalex.org/I44854399","display_name":"University of Southern Mississippi","ror":"https://ror.org/0270vfa57","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I44854399"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chaoyang Zhang","raw_affiliation_strings":["School of Computing Sciences and Computer Engineering, University of Southern Mississippi, 118 College Drive, Hattiesburg, MS, 39406, USA"],"affiliations":[{"raw_affiliation_string":"School of Computing Sciences and Computer Engineering, University of Southern Mississippi, 118 College Drive, Hattiesburg, MS, 39406, USA","institution_ids":["https://openalex.org/I44854399"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100401133","display_name":"Zheng Wang","orcid":"https://orcid.org/0000-0002-9330-0728"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zheng Wang","raw_affiliation_strings":["Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral Gables, FL, 33124, USA. zheng.wang@miami.edu","Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral Gables, FL, 33124, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral Gables, FL, 33124, USA. zheng.wang@miami.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, University of Miami, 1365 Memorial Drive, Coral Gables, FL, 33124, USA","institution_ids":["https://openalex.org/I145608581"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5011631125"],"corresponding_institution_ids":["https://openalex.org/I44854399"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6871,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.68464133,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"S2","first_page":"100","last_page":"100"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T12254","display_name":"Machine Learning in Bioinformatics","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/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9943000078201294,"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/residue","display_name":"Residue (chemistry)","score":0.803337037563324},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.47957056760787964},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47401103377342224},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4043576717376709},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3253660500049591},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23838946223258972},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17609566450119019},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.17234304547309875}],"concepts":[{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.803337037563324},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.47957056760787964},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47401103377342224},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4043576717376709},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3253660500049591},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23838946223258972},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17609566450119019},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17234304547309875}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":"Q000592","qualifier_name":"standards","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":"D000595","descriptor_name":"Amino Acid Sequence","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":"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":6,"locations":[{"id":"doi:10.1186/s12859-019-2627-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2627-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2627-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30871477","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30871477","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:aquila.usm.edu:fac_pubs-17295","is_oa":true,"landing_page_url":"https://aquila.usm.edu/fac_pubs/15984","pdf_url":"https://aquila.usm.edu/cgi/viewcontent.cgi?article=17295&context=fac_pubs","source":{"id":"https://openalex.org/S4306402529","display_name":"Aquila Digital Community (University of Southern Mississippi)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I44854399","host_organization_name":"University of Southern Mississippi","host_organization_lineage":["https://openalex.org/I44854399"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:8502c0180ade446fa4399abe6ca4b2a3","is_oa":true,"landing_page_url":"https://doaj.org/article/8502c0180ade446fa4399abe6ca4b2a3","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss S2, Pp 115-127 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5415857","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6419322","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6419322","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6419322","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2627-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2627-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2627-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7300000190734863,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G6482736948","display_name":null,"funder_award_id":"start-up","funder_id":"https://openalex.org/F4320309249","funder_display_name":"University of Miami"},{"id":"https://openalex.org/G809689749","display_name":null,"funder_award_id":"R15GM120650","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309249","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2921356781.pdf","grobid_xml":"https://content.openalex.org/works/W2921356781.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W273955616","https://openalex.org/W1967195968","https://openalex.org/W1967292572","https://openalex.org/W1994983243","https://openalex.org/W2002129624","https://openalex.org/W2008545402","https://openalex.org/W2018363141","https://openalex.org/W2033354942","https://openalex.org/W2047774682","https://openalex.org/W2051210555","https://openalex.org/W2060107523","https://openalex.org/W2096495474","https://openalex.org/W2103967716","https://openalex.org/W2106116715","https://openalex.org/W2119550029","https://openalex.org/W2127322768","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2137965757","https://openalex.org/W2142529984","https://openalex.org/W2145957695","https://openalex.org/W2160784118","https://openalex.org/W2176135968","https://openalex.org/W2343039591","https://openalex.org/W2385735394","https://openalex.org/W2417306259","https://openalex.org/W2471276590","https://openalex.org/W2605518777","https://openalex.org/W2949867299","https://openalex.org/W2951621517"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834","https://openalex.org/W657579294"],"abstract_inverted_index":{"Due":[0],"to":[1,11,36,46,75],"the":[2,55,76],"challenging":[3],"nature":[4],"of":[5,17,54],"contact":[6,34],"prediction,":[7],"it":[8],"is":[9],"beneficial":[10],"develop":[12],"and":[13,67],"benchmark":[14],"a":[15,28,40,60],"variety":[16],"different":[18],"prediction":[19],"methods.":[20],"Our":[21],"work":[22],"has":[23],"produced":[24],"useful":[25],"tools":[26],"with":[27],"simple":[29],"interface":[30],"that":[31],"can":[32],"provide":[33],"predictions":[35],"users":[37],"without":[38],"requiring":[39],"lengthy":[41],"installation":[42],"process.":[43],"In":[44],"addition":[45],"this,":[47],"we":[48],"have":[49],"released":[50],"our":[51,68],"C++":[52],"implementation":[53],"direct-coupling":[56],"analysis":[57],"method":[58],"as":[59],"standalone":[61],"software":[62],"package.":[63],"Both":[64],"this":[65],"tool":[66],"RFcon":[69],"web":[70],"server":[71],"are":[72],"freely":[73],"available":[74],"public":[77],"at":[78],"http://dna.cs.miami.edu/RFcon":[79],"/.":[80]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
