{"id":"https://openalex.org/W2142765985","doi":"https://doi.org/10.1142/s0219720009004400","title":"EXPLORING THE PROTEIN LANDSCAPE IN RAMACHANDRAN SPACE: IT'S NOT JUST PSI-PHI","display_name":"EXPLORING THE PROTEIN LANDSCAPE IN RAMACHANDRAN SPACE: IT'S NOT JUST PSI-PHI","publication_year":2009,"publication_date":"2009-12-01","ids":{"openalex":"https://openalex.org/W2142765985","doi":"https://doi.org/10.1142/s0219720009004400","mag":"2142765985","pmid":"https://pubmed.ncbi.nlm.nih.gov/20014477"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720009004400","doi":"https://doi.org/10.1142/s0219720009004400","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720009004400","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,"listed_in":["cwts-core","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-40","russia-white-list-2","vabb-shw"],"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"},"volume":null,"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/A5024035395","display_name":"William Krivan","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"WILLIAM KRIVAN","raw_affiliation_strings":["Protein Advances, Inc. (Protein AI), 1102 Columbia Street, Suite 110, Seattle, Washington 98104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Protein Advances, Inc. (Protein AI), 1102 Columbia Street, Suite 110, Seattle, Washington 98104, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072667047","display_name":"Darrick Carter","orcid":"https://orcid.org/0000-0001-5901-3402","observed_orcids":["https://orcid.org/0000-0001-5901-3402"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"DARRICK CARTER","raw_affiliation_strings":["Protein Advances, Inc. (Protein AI), 1102 Columbia Street, Suite 110, Seattle, Washington 98104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Protein Advances, Inc. (Protein AI), 1102 Columbia Street, Suite 110, Seattle, Washington 98104, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.18273741,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"07","issue":"06","first_page":"1031","last_page":"1037"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9976000189781189,"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":0.9976000189781189,"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":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/backbone-torsion-angles","display_name":"backbone torsion angles","score":0.9959999918937683},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"protein structure database","score":0.515999972820282}],"concepts":[{"id":"https://openalex.org/C14301744","wikidata":"https://www.wikidata.org/wiki/Q579211","display_name":"Ramachandran plot","level":3,"score":0.9801197052001953},{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.6467530727386475},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5002155303955078},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.48370271921157837},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.4755915403366089},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46328821778297424},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42239224910736084},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.32295769453048706},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31350210309028625},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.2628887891769409},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.20737317204475403},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14850246906280518},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720009004400","doi":"https://doi.org/10.1142/s0219720009004400","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720009004400","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,"listed_in":["cwts-core","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-40","russia-white-list-2","vabb-shw"],"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:20014477","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20014477","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,"listed_in":[],"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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/11","display_name":"Sustainable cities and communities","score":0.5699999928474426}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1964499168","https://openalex.org/W2022058405","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2130479394","https://openalex.org/W2144998676","https://openalex.org/W2150434889","https://openalex.org/W2152326664","https://openalex.org/W4239146293"],"related_works":["https://openalex.org/W2139753312","https://openalex.org/W4321996907","https://openalex.org/W85537610","https://openalex.org/W2034132992","https://openalex.org/W2117699649","https://openalex.org/W1562243078","https://openalex.org/W2771465500","https://openalex.org/W4380266100","https://openalex.org/W2051059399","https://openalex.org/W2141921185"],"abstract_inverted_index":{"Most":[0],"methods":[1],"for":[2],"the":[3,12,27,67,77,82,85,95,98,102],"structural":[4,58],"comparison":[5],"of":[6,29,34,57,84,108,118],"proteins":[7],"utilize":[8],"molecular":[9],"coordinates":[10],"in":[11,32,43,122],"three-dimensional":[13],"physical":[14],"space.":[15,124],"Recently,":[16],"a":[17,114],"group":[18],"has":[19],"presented":[20],"an":[21],"elegant":[22],"novel":[23],"approach":[24,70],"based":[25],"on":[26],"characterization":[28],"protein":[30],"shape":[31],"terms":[33],"backbone":[35],"torsion":[36,68],"angles.":[37],"They":[38],"have":[39],"demonstrated":[40],"considerable":[41],"success":[42],"direct":[44],"comparisons":[45],"with":[46],"other":[47],"techniques,":[48],"and":[49,110],"their":[50],"method":[51],"lends":[52],"itself":[53],"to":[54,93],"rapid":[55],"screening":[56],"information":[59],"from":[60],"rapidly":[61],"growing":[62],"databases.":[63],"We":[64],"think":[65],"that":[66,80,100],"angle":[69],"can":[71],"be":[72],"further":[73],"strengthened":[74],"by":[75],"refining":[76],"distance":[78,96],"notion":[79],"forms":[81],"basis":[83],"computational":[86],"scheme.":[87],"In":[88],"particular,":[89],"we":[90],"are":[91],"suggesting":[92],"compute":[94],"along":[97],"path":[99],"minimizes":[101],"transition":[103],"cost":[104],"between":[105,120],"aligned":[106],"pairs":[107],"angles":[109],"therefore":[111],"likely":[112],"provides":[113],"more":[115],"meaningful":[116],"representation":[117],"distances":[119],"points":[121],"Ramachandran":[123]},"counts_by_year":[],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}