{"id":"https://openalex.org/W2042786254","doi":"https://doi.org/10.1109/bibe.2007.4375651","title":"Amino Acid Substitution Matrices Based on 4-Body Delaunay Contact Profiles","display_name":"Amino Acid Substitution Matrices Based on 4-Body Delaunay Contact Profiles","publication_year":2007,"publication_date":"2007-10-01","ids":{"openalex":"https://openalex.org/W2042786254","doi":"https://doi.org/10.1109/bibe.2007.4375651","mag":"2042786254"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2007.4375651","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375651","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/11511/46827","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016398897","display_name":"Ahmet Sa\u00e7an","orcid":"https://orcid.org/0000-0002-3570-3270"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ahmet Sacan","raw_affiliation_strings":["Computer Engineering Department, Middle East Technical University, Ankara, Turkey","Middle East Techn. Univ., Ankara"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Department, Middle East Technical University, Ankara, Turkey","institution_ids":["https://openalex.org/I201799495"]},{"raw_affiliation_string":"Middle East Techn. Univ., Ankara","institution_ids":["https://openalex.org/I201799495"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039253696","display_name":"\u0130smail Hakk\u0131 Toroslu","orcid":"https://orcid.org/0000-0002-4524-8232"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"I. Hakki Toroslu","raw_affiliation_strings":["Computer Engineering Department, Middle East Technical University, Ankara, Turkey","Middle East Techn. Univ., Ankara"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Department, Middle East Technical University, Ankara, Turkey","institution_ids":["https://openalex.org/I201799495"]},{"raw_affiliation_string":"Middle East Techn. Univ., Ankara","institution_ids":["https://openalex.org/I201799495"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I201799495"],"apc_list":null,"apc_paid":null,"fwci":4.2112,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.93302847,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"5","issue":null,"first_page":"796","last_page":"801"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9969000220298767,"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/substitution","display_name":"Substitution (logic)","score":0.6769828796386719},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5284445285797119},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5245984792709351},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5236392021179199},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5095365643501282},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4939737915992737},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.48271557688713074},{"id":"https://openalex.org/keywords/distance-matrix","display_name":"Distance matrix","score":0.4665985107421875},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4332994222640991},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32710403203964233},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2647166848182678},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25661763548851013},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16414675116539001},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12422344088554382},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10789370536804199},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08799949288368225},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0750143826007843}],"concepts":[{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.6769828796386719},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5284445285797119},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5245984792709351},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5236392021179199},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5095365643501282},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4939737915992737},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.48271557688713074},{"id":"https://openalex.org/C111208986","wikidata":"https://www.wikidata.org/wiki/Q901698","display_name":"Distance matrix","level":2,"score":0.4665985107421875},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4332994222640991},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32710403203964233},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2647166848182678},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25661763548851013},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16414675116539001},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12422344088554382},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10789370536804199},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08799949288368225},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0750143826007843},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","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/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibe.2007.4375651","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2007.4375651","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE 7th International Symposium on BioInformatics and BioEngineering","raw_type":"proceedings-article"},{"id":"pmh:oai:open.metu.edu.tr:11511/46827","is_oa":true,"landing_page_url":"https://hdl.handle.net/11511/46827","pdf_url":null,"source":{"id":"https://openalex.org/S4306402495","display_name":"OpenMETU (Middle East Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201799495","host_organization_name":"Middle East Technical University","host_organization_lineage":["https://openalex.org/I201799495"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference Paper"}],"best_oa_location":{"id":"pmh:oai:open.metu.edu.tr:11511/46827","is_oa":true,"landing_page_url":"https://hdl.handle.net/11511/46827","pdf_url":null,"source":{"id":"https://openalex.org/S4306402495","display_name":"OpenMETU (Middle East Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201799495","host_organization_name":"Middle East Technical University","host_organization_lineage":["https://openalex.org/I201799495"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference Paper"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8700000047683716}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W171003663","https://openalex.org/W1485790693","https://openalex.org/W1558365920","https://openalex.org/W1566039206","https://openalex.org/W1966041739","https://openalex.org/W1998479488","https://openalex.org/W2004575181","https://openalex.org/W2044128233","https://openalex.org/W2044573154","https://openalex.org/W2063619185","https://openalex.org/W2068519185","https://openalex.org/W2074231493","https://openalex.org/W2081899468","https://openalex.org/W2087064593","https://openalex.org/W2097138244","https://openalex.org/W2103487267","https://openalex.org/W2103612114","https://openalex.org/W2121150070","https://openalex.org/W2123956446","https://openalex.org/W2130179054","https://openalex.org/W2131239524","https://openalex.org/W2143210482","https://openalex.org/W2144472358","https://openalex.org/W2153504150","https://openalex.org/W2158714788","https://openalex.org/W2162017027","https://openalex.org/W2163860567","https://openalex.org/W2168211076","https://openalex.org/W2168795207","https://openalex.org/W4253539230","https://openalex.org/W6633291510","https://openalex.org/W6641560652"],"related_works":["https://openalex.org/W2029514038","https://openalex.org/W2088487249","https://openalex.org/W2111937814","https://openalex.org/W2051969447","https://openalex.org/W1985408726","https://openalex.org/W2061567716","https://openalex.org/W2130940308","https://openalex.org/W2084367350","https://openalex.org/W2188796099","https://openalex.org/W2802438627"],"abstract_inverted_index":{"Sequence":[0],"similarity":[1],"search":[2,32],"of":[3,7,30,36,62,84,92,112,122,139],"proteins":[4],"is":[5,19,96,105],"one":[6],"the":[8,31,34,37,43,99,116,119,137],"basic":[9],"and":[10,18,25,33,104,144,154],"most":[11],"common":[12],"steps":[13],"followed":[14],"in":[15,21,64,136,145],"bioninformatics":[16],"research":[17],"used":[20],"making":[22],"evolutionary,":[23],"structural,":[24],"functional":[26],"inferences.":[27],"The":[28,89],"quality":[29],"alignment":[35,83,90,102,156],"protein":[38,66,85],"sequences":[39,86],"depend":[40],"crucially":[41],"on":[42,77],"underlying":[44],"amino-acid":[45],"substitution":[46,56,152],"matrix.":[47],"We":[48],"present":[49],"a":[50],"method":[51,73],"for":[52],"deriving":[53],"amino":[54],"acid":[55],"matrices":[57,95,114,124,131,153],"from":[58,115,161],"4-body":[59],"contact":[60],"propensities":[61],"amino-acids":[63],"3D":[65],"structures.":[67,88],"Unlike":[68],"current":[69],"popular":[70,113],"methods,":[71],"our":[72,93,123],"does":[74],"not":[75],"rely":[76],"mutational":[78],"analysis,":[79],"evolutionary":[80],"arguments,":[81],"or":[82,87],"accuracy":[91],"derived":[94],"evaluated":[97],"using":[98],"BAliBASE":[100],"reference":[101],"set":[103],"found":[106],"to":[107,110],"be":[108,133,159],"comparable":[109],"that":[111],"literature.":[117],"Notably,":[118],"metric":[120,128],"subset":[121],"outperform":[125],"other":[126],"available":[127],"matrices.":[129],"Our":[130,151],"will":[132],"useful":[134],"especially":[135],"development":[138],"empirical":[140],"potential":[141],"energy":[142],"functions":[143],"distance-based":[146],"sequence":[147],"indexing.":[148],"Supplementary":[149],"Material:":[150],"detailed":[155],"data":[157],"can":[158],"obtained":[160],"http://www.ceng.metu.edu.tr/~ahmet/bioinfo/distmat":[162]},"counts_by_year":[{"year":2015,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
