{"id":"https://openalex.org/W2026122721","doi":"https://doi.org/10.1142/s0219720010004501","title":"TOPTMH: TOPOLOGY PREDICTOR FOR TRANSMEMBRANE \u03b1-HELICES","display_name":"TOPTMH: TOPOLOGY PREDICTOR FOR TRANSMEMBRANE \u03b1-HELICES","publication_year":2010,"publication_date":"2010-02-01","ids":{"openalex":"https://openalex.org/W2026122721","doi":"https://doi.org/10.1142/s0219720010004501","mag":"2026122721","pmid":"https://pubmed.ncbi.nlm.nih.gov/20183873"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720010004501","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010004501","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5086696236","display_name":"Rezwan Ahmed","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"REZWAN AHMED","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006581225","display_name":"Huzefa Rangwala","orcid":"https://orcid.org/0000-0003-0435-0035"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"HUZEFA RANGWALA","raw_affiliation_strings":["Department of Computer Science, George Mason University, Fairfax, Virginia 22030, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, George Mason University, Fairfax, Virginia 22030, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082384108","display_name":"George Karypis","orcid":"https://orcid.org/0000-0003-2753-1437"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"GEORGE KARYPIS","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5086696236"],"corresponding_institution_ids":["https://openalex.org/I130238516"],"apc_list":null,"apc_paid":null,"fwci":0.793,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.70554248,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"08","issue":"01","first_page":"39","last_page":"57"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9987000226974487,"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":0.9933000206947327,"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/computer-science","display_name":"Computer science","score":0.6309232115745544},{"id":"https://openalex.org/keywords/transmembrane-domain","display_name":"Transmembrane domain","score":0.5710344314575195},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.567942202091217},{"id":"https://openalex.org/keywords/transmembrane-protein","display_name":"Transmembrane protein","score":0.5424140691757202},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5349297523498535},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4878716468811035},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.47525784373283386},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.46223124861717224},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.45163968205451965},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.4303986728191376},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4198802411556244},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3910711407661438},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3725520372390747},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.36201339960098267},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3494367003440857},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33207178115844727},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3175885081291199},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.25625357031822205},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17815521359443665},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1288074254989624},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11943411827087402}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6309232115745544},{"id":"https://openalex.org/C118892022","wikidata":"https://www.wikidata.org/wiki/Q7834587","display_name":"Transmembrane domain","level":3,"score":0.5710344314575195},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.567942202091217},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.5424140691757202},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5349297523498535},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4878716468811035},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.47525784373283386},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.46223124861717224},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.45163968205451965},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4303986728191376},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4198802411556244},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3910711407661438},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3725520372390747},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.36201339960098267},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3494367003440857},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33207178115844727},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3175885081291199},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.25625357031822205},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17815521359443665},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1288074254989624},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11943411827087402},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720010004501","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010004501","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:20183873","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20183873","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 bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1526754730","https://openalex.org/W1576520375","https://openalex.org/W1971147414","https://openalex.org/W1975304761","https://openalex.org/W2005584853","https://openalex.org/W2009330288","https://openalex.org/W2025859600","https://openalex.org/W2046267877","https://openalex.org/W2074266029","https://openalex.org/W2087009455","https://openalex.org/W2097775366","https://openalex.org/W2097870001","https://openalex.org/W2098994369","https://openalex.org/W2101466114","https://openalex.org/W2109261827","https://openalex.org/W2114068014","https://openalex.org/W2114083522","https://openalex.org/W2115840790","https://openalex.org/W2117919289","https://openalex.org/W2120684043","https://openalex.org/W2125084853","https://openalex.org/W2125838338","https://openalex.org/W2130479394","https://openalex.org/W2142893109","https://openalex.org/W2143814286","https://openalex.org/W2144112248","https://openalex.org/W2152770371","https://openalex.org/W2156125289","https://openalex.org/W2156693221","https://openalex.org/W2158613515","https://openalex.org/W2158714788","https://openalex.org/W2158906453","https://openalex.org/W2159136327","https://openalex.org/W2161062388","https://openalex.org/W2161911785","https://openalex.org/W2163137692","https://openalex.org/W3202211045"],"related_works":["https://openalex.org/W3099772455","https://openalex.org/W3172198228","https://openalex.org/W1986078734","https://openalex.org/W2129301794","https://openalex.org/W1540599686","https://openalex.org/W2016396528","https://openalex.org/W2033001120","https://openalex.org/W2261012589","https://openalex.org/W4377101717","https://openalex.org/W1605284188"],"abstract_inverted_index":{"Alpha-helical":[0],"transmembrane":[1,37,50,114],"proteins":[2],"mediate":[3],"many":[4,15],"key":[5],"biological":[6],"processes":[7],"and":[8,34,63,93,107,130],"represent":[9],"20%-30%":[10],"of":[11,36,71,77,99,122],"all":[12],"genes":[13],"in":[14,21],"organisms.":[16],"Due":[17],"to":[18,30,88,110],"the":[19,32,75,90,104,112,119,132],"difficulties":[20],"experimentally":[22],"determining":[23],"their":[24],"high-resolution":[25],"3D":[26],"structure,":[27],"computational":[28],"methods":[29,129],"predict":[31,89],"location":[33],"orientation":[35],"helix":[38,51,91,115],"segments":[39,116],"using":[40],"sequence":[41],"information":[42],"are":[43],"essential.":[44],"We":[45],"present":[46],"TOPTMH,":[47],"a":[48,64,78,84,97],"new":[49],"topology":[52],"prediction":[53,79,128],"method":[54],"that":[55,81,102],"combines":[56],"support":[57],"vector":[58],"machines,":[59],"hidden":[60],"Markov":[61],"models,":[62],"widely":[65],"used":[66],"rule-based":[67],"scheme.":[68],"The":[69],"contribution":[70],"this":[72],"work":[73],"is":[74],"development":[76],"approach":[80],"first":[82],"uses":[83],"binary":[85],"SVM":[86,105],"classifier":[87],"residues":[92],"then":[94],"it":[95],"employs":[96],"pair":[98],"HMM":[100],"models":[101],"incorporate":[103],"predictions":[106],"hydropathy-based":[108],"features":[109],"identify":[111],"entire":[113],"by":[117],"capturing":[118],"structural":[120],"characteristics":[121],"these":[123],"proteins.":[124],"TOPTMH":[125],"outperforms":[126],"state-of-the-art":[127],"achieves":[131],"best":[133],"performance":[134],"on":[135],"an":[136],"independent":[137],"static":[138],"benchmark.":[139]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}