{"id":"https://openalex.org/W2008271273","doi":"https://doi.org/10.1109/bibm.2012.6392666","title":"Improving interacting residue prediction using long-distance information in hidden Markov models","display_name":"Improving interacting residue prediction using long-distance information in hidden Markov models","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W2008271273","doi":"https://doi.org/10.1109/bibm.2012.6392666","mag":"2008271273"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2012.6392666","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2012.6392666","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5047261789","display_name":"Colin Kern","orcid":"https://orcid.org/0000-0002-3249-6405"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Colin Kern","raw_affiliation_strings":["Department of Computer and Information Science, University of Delaware, Newark, DE, USA","Department of Computer and Information Science, University of Delaware, Newark, DE 19716, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Science, University of Delaware, Newark, DE 19716, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051925857","display_name":"\u00c1lvaro Gonz\u00e1lez","orcid":"https://orcid.org/0000-0002-1423-273X"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alvaro J. Gonzalez","raw_affiliation_strings":["Department of Computer and Information Science, University of Delaware, Newark, DE, USA","Department of Computer and Information Science, University of Delaware, Newark, DE 19716, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Science, University of Delaware, Newark, DE 19716, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101595032","display_name":"Li Liao","orcid":"https://orcid.org/0000-0002-1197-1879"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li Liao","raw_affiliation_strings":["Department of Computer and Information Science, University of Delaware, Newark, DE, USA","Department of Computer and Information Science, University of Delaware, Newark, DE 19716, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Science, University of Delaware, Newark, DE 19716, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027009667","display_name":"K. Vijay\u2010Shanker","orcid":"https://orcid.org/0000-0003-0958-3073"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K. Vijay-Shanker","raw_affiliation_strings":["Department of Computer and Information Science, University of Delaware, Newark, DE, USA","Department of Computer and Information Science, University of Delaware, Newark, DE 19716, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, University of Delaware, Newark, DE, USA","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Computer and Information Science, University of Delaware, Newark, DE 19716, USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5047261789"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06784648,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"34","issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9972000122070312,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9972000122070312,"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/hidden-markov-model","display_name":"Hidden Markov model","score":0.7141762375831604},{"id":"https://openalex.org/keywords/viterbi-algorithm","display_name":"Viterbi algorithm","score":0.7008060216903687},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6476341485977173},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5729449391365051},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.5008172988891602},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.49860596656799316},{"id":"https://openalex.org/keywords/markov-model","display_name":"Markov model","score":0.48510777950286865},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45631465315818787},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.43519580364227295},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.43278688192367554},{"id":"https://openalex.org/keywords/markov-process","display_name":"Markov process","score":0.41724666953086853},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.41580620408058167},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4040653109550476},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3548464775085449},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.29360538721084595},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20353367924690247},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.11900106072425842}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.7141762375831604},{"id":"https://openalex.org/C60582962","wikidata":"https://www.wikidata.org/wiki/Q83886","display_name":"Viterbi algorithm","level":3,"score":0.7008060216903687},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6476341485977173},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5729449391365051},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.5008172988891602},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.49860596656799316},{"id":"https://openalex.org/C163836022","wikidata":"https://www.wikidata.org/wiki/Q6771326","display_name":"Markov model","level":3,"score":0.48510777950286865},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45631465315818787},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.43519580364227295},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.43278688192367554},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.41724666953086853},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.41580620408058167},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4040653109550476},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3548464775085449},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.29360538721084595},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20353367924690247},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.11900106072425842},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2012.6392666","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2012.6392666","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320314254","display_name":"Delaware IDeA Network of Biomedical Research Excellence","ror":null},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1988422871","https://openalex.org/W2054291744","https://openalex.org/W2065304353","https://openalex.org/W2079712952","https://openalex.org/W2102122585","https://openalex.org/W2105594594","https://openalex.org/W2122369731","https://openalex.org/W2136280642","https://openalex.org/W2137329336","https://openalex.org/W2151831732","https://openalex.org/W2161911785","https://openalex.org/W2162354472","https://openalex.org/W3150945973","https://openalex.org/W4245668478","https://openalex.org/W6678068712","https://openalex.org/W6683814780"],"related_works":["https://openalex.org/W2136652457","https://openalex.org/W2169849734","https://openalex.org/W2129150969","https://openalex.org/W2236912844","https://openalex.org/W1975869217","https://openalex.org/W2401728283","https://openalex.org/W2383829109","https://openalex.org/W2386035178","https://openalex.org/W2116722627","https://openalex.org/W2379938888"],"abstract_inverted_index":{"Identification":[0],"of":[1,17,74,105],"interacting":[2,59,117],"residues":[3,60,118],"involved":[4],"in":[5,87,99],"protein-protein":[6],"and":[7,15,20,26,69,82,94,122],"protein-ligand":[8],"interaction":[9,19,46,76],"is":[10],"critical":[11],"for":[12],"the":[13,18,55,79,96,101,110,127,132],"prediction":[14,63,128],"understanding":[16],"has":[21],"practical":[22],"impact":[23],"on":[24,109],"mutagenesis":[25],"drug":[27],"design.":[28],"In":[29],"this":[30],"work,":[31],"we":[32],"introduce":[33],"a":[34,72],"new":[35],"decoding":[36],"algorithm,":[37],"ETB-Viterbi,":[38],"with":[39,113],"early":[40],"trace":[41],"back":[42],"mechanism":[43],"built":[44],"into":[45],"profile":[47],"hidden":[48],"Markov":[49],"models":[50],"(ipHMMs)":[51],"that":[52,126],"can":[53],"incorporate":[54],"long-distance":[56],"correlations":[57,133],"between":[58,116],"to":[61,71],"improve":[62],"accuracy.":[64],"The":[65],"method":[66],"was":[67,124],"applied":[68],"tested":[70],"set":[73],"domain-domain":[75],"families":[77],"from":[78],"3DID":[80,111],"database,":[81],"showed":[83],"statistically":[84],"significant":[85],"improvement":[86],"accuracy":[88],"measured":[89],"by":[90],"F-score.":[91],"To":[92],"gauge":[93],"assess":[95],"method's":[97],"effectiveness":[98],"capturing":[100],"correlation":[102,115],"signals,":[103],"sets":[104],"simulated":[106],"data":[107],"based":[108],"dataset":[112],"controllable":[114],"were":[119],"also":[120],"used,":[121],"it":[123],"demonstrated":[125],"consistently":[129],"improves":[130],"as":[131],"increase.":[134]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}