{"id":"https://openalex.org/W1579786457","doi":null,"title":"Protein Structure Prediction By Threading: Force Field Philosophy, Approaches to Alignment","display_name":"Protein Structure Prediction By Threading: Force Field Philosophy, Approaches to Alignment","publication_year":2001,"publication_date":"2001-01-01","ids":{"openalex":"https://openalex.org/W1579786457","mag":"1579786457"},"language":"en","primary_location":{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1.6907","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.6907","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.zbh.uni-hamburg.de/research/BM/torda/papers/book_tsigelny.pdf","raw_type":"text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"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/A5076677952","display_name":"Thomas Huber","orcid":"https://orcid.org/0000-0002-3680-8699","observed_orcids":["https://orcid.org/0000-0002-3680-8699"]},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Thomas Huber","raw_affiliation_strings":["Australian National University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian National University","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002244022","display_name":"Andrew E. Torda","orcid":"https://orcid.org/0000-0002-6076-709X","observed_orcids":["https://orcid.org/0000-0002-6076-709X"]},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Andrew E. Torda","raw_affiliation_strings":["Australian National University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian National University","institution_ids":["https://openalex.org/I118347636"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I118347636"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980000257492065,"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":0.9980000257492065,"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/T11162","display_name":"Enzyme Structure and Function","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10211","display_name":"Computational Drug Discovery Methods","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"protein structure prediction","score":0.9459999799728394},{"id":"https://openalex.org/keywords/threading","display_name":"threading","score":0.7519999742507935},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"homology modeling","score":0.703000009059906},{"id":"https://openalex.org/keywords/force-fields","display_name":"force fields","score":0.847000002861023},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"sequence alignment","score":0.753000020980835},{"id":"https://openalex.org/keywords/conformational-space","display_name":"conformational space","score":0.7279999852180481},{"id":"https://openalex.org/keywords/score-function","display_name":"score function","score":0.6970000267028809},{"id":"https://openalex.org/keywords/free-energy-landscape","display_name":"free energy landscape","score":0.44600000977516174},{"id":"https://openalex.org/keywords/conformational-search","display_name":"conformational search","score":0.5590000152587891}],"concepts":[{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.9036791324615479},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.6818978786468506},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.5678004026412964},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4286423325538635},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3777444362640381},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3364490270614624},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2513520121574402},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18318960070610046},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1088072657585144},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.09167695045471191},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1.6907","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.6907","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.zbh.uni-hamburg.de/research/BM/torda/papers/book_tsigelny.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":83,"referenced_works":["https://openalex.org/W1188919047","https://openalex.org/W1503558940","https://openalex.org/W1535631466","https://openalex.org/W1589812083","https://openalex.org/W1965824601","https://openalex.org/W1970812247","https://openalex.org/W1975017420","https://openalex.org/W1986466512","https://openalex.org/W1996159969","https://openalex.org/W1996470926","https://openalex.org/W2001956250","https://openalex.org/W2003853681","https://openalex.org/W2009822822","https://openalex.org/W2012534919","https://openalex.org/W2019475286","https://openalex.org/W2021953523","https://openalex.org/W2022320562","https://openalex.org/W2024060531","https://openalex.org/W2027071679","https://openalex.org/W2027408247","https://openalex.org/W2028931227","https://openalex.org/W2029699793","https://openalex.org/W2033496784","https://openalex.org/W2033806446","https://openalex.org/W2035888722","https://openalex.org/W2037928576","https://openalex.org/W2038863293","https://openalex.org/W2040594319","https://openalex.org/W2041966417","https://openalex.org/W2043774984","https://openalex.org/W2045950270","https://openalex.org/W2046001409","https://openalex.org/W2047477476","https://openalex.org/W2049357790","https://openalex.org/W2050330741","https://openalex.org/W2050625197","https://openalex.org/W2055043387","https://openalex.org/W2058336694","https://openalex.org/W2060100112","https://openalex.org/W2060778016","https://openalex.org/W2064721029","https://openalex.org/W2067291595","https://openalex.org/W2071884199","https://openalex.org/W2077520867","https://openalex.org/W2082169035","https://openalex.org/W2082621844","https://openalex.org/W2085764610","https://openalex.org/W2088404992","https://openalex.org/W2088502819","https://openalex.org/W2088848851","https://openalex.org/W2090847673","https://openalex.org/W2097555181","https://openalex.org/W2104972430","https://openalex.org/W2110879595","https://openalex.org/W2111193871","https://openalex.org/W2122199548","https://openalex.org/W2122665495","https://openalex.org/W2123768455","https://openalex.org/W2124871329","https://openalex.org/W2130161623","https://openalex.org/W2132883011","https://openalex.org/W2133715954","https://openalex.org/W2135580377","https://openalex.org/W2137345862","https://openalex.org/W2139279375","https://openalex.org/W2139582206","https://openalex.org/W2140244239","https://openalex.org/W2142727530","https://openalex.org/W2143210482","https://openalex.org/W2144483796","https://openalex.org/W2146610289","https://openalex.org/W2146760785","https://openalex.org/W2148521301","https://openalex.org/W2149612698","https://openalex.org/W2151831732","https://openalex.org/W2153187042","https://openalex.org/W2155479906","https://openalex.org/W2155972356","https://openalex.org/W2158714788","https://openalex.org/W2164308539","https://openalex.org/W2166728082","https://openalex.org/W2171641243","https://openalex.org/W3147254695"],"related_works":["https://openalex.org/W2142727530","https://openalex.org/W4251972613","https://openalex.org/W2063058848","https://openalex.org/W3105292938","https://openalex.org/W2590393821","https://openalex.org/W2054260513","https://openalex.org/W7100333167","https://openalex.org/W2064336918","https://openalex.org/W7097456857","https://openalex.org/W7066269455"],"abstract_inverted_index":{"Introduction":[0],"If":[1,71],"you":[2,8,14,31,72,95,108],"are":[3,40,73,164],"given":[4],"a":[5,81,138],"protein's":[6],"sequence,":[7],"might":[9,54,88],"have":[10,21,33,109,111],"all":[11],"the":[12,22,28,43,49,67,77,152,168],"information":[13],"need":[15],"to":[16,34,75,110,133,135,151],"predict":[17],"its":[18,36],"structure.":[19],"You":[20],"composition":[23],"and":[24,48,123,147],"(bond)":[25],"topology":[26],"of":[27,69,145,155],"system,":[29],"so":[30,38],"only":[32,165],"rearrange":[35],"atoms":[37,141],"they":[39],"somewhere":[41],"in":[42],"major":[44],"free":[45],"energy":[46,113],"basin":[47],"problem":[50],"is":[51,103,130,158],"solved.":[52],"There":[53],"be":[55,89,143],"some":[56],"problems":[57],"with":[58,66],"this":[59,85],"approach.":[60],"The":[61],"search":[62,76],"space":[63,79],"grows":[64],"exponentially":[65],"number":[68],"particles.":[70],"able":[74],"conformational":[78],"for":[80],"five":[82],"residue":[83],"peptide":[84],"year,":[86],"it":[87],"another":[90],"year":[91],"or":[92,114],"two":[93],"until":[94],"can":[96,119],"tackle":[97],"six":[98],"residues":[99],"when":[100],"your":[101],"computer":[102],"several":[104],"fold":[105],"faster.":[106],"Then,":[107],"an":[112],"score":[115,127],"function":[116,128],"which":[117,129],"really":[118],"discriminate":[120],"between":[121],"correct":[122],"incorrect":[124],"conformations.":[125],"Any":[126],"fast":[131],"enough":[132],"apply":[134],"more":[136],"than":[137],"few":[139],"hundred":[140],"will":[142],"full":[144],"approximations":[146],"no":[148],"longer":[149],"close":[150],"best":[153],"level":[154],"theory.":[156],"It":[157],"also":[159],"worth":[160],"remembering":[161],"that":[162,167],"we":[163],"assuming":[166],"native":[169],"protein":[170],"conformat":[171]},"counts_by_year":[],"updated_date":"2026-10-10T09:11:00.788812","created_date":"2016-06-24T00:00:00"}
