{"id":"https://openalex.org/W2154237723","doi":"https://doi.org/10.1093/bioinformatics/btl538","title":"PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory","display_name":"PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory","publication_year":2006,"publication_date":"2006-10-24","ids":{"openalex":"https://openalex.org/W2154237723","doi":"https://doi.org/10.1093/bioinformatics/btl538","mag":"2154237723","pmid":"https://pubmed.ncbi.nlm.nih.gov/17062588"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl538","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl538","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/1/99/49816261/bioinformatics_23_1_99.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/23/1/99/49816261/bioinformatics_23_1_99.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078014032","display_name":"Ruhong Zhou","orcid":"https://orcid.org/0000-0001-8624-5591"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ruhong Zhou","raw_affiliation_strings":["Computational Biology Center, IBM T. J. Watson Research Center 1 \u00a0 1 \u00a0 \u00a0 Yorktown Heights, NY 10598, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, IBM T. J. Watson Research Center 1 \u00a0 1 \u00a0 \u00a0 Yorktown Heights, NY 10598, USA","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025497346","display_name":"Laxmi Parida","orcid":"https://orcid.org/0000-0002-7872-5074"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laxmi Parida","raw_affiliation_strings":["Computational Biology Center, IBM T. J. Watson Research Center 1 \u00a0 1 \u00a0 \u00a0 Yorktown Heights, NY 10598, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Center, IBM T. J. Watson Research Center 1 \u00a0 1 \u00a0 \u00a0 Yorktown Heights, NY 10598, USA","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058869299","display_name":"Kush Kapila","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kush Kapila","raw_affiliation_strings":["Matrox Imaging Inc., Dorval 2 \u00a0 2 \u00a0 \u00a0 Quebec, Canada"],"affiliations":[{"raw_affiliation_string":"Matrox Imaging Inc., Dorval 2 \u00a0 2 \u00a0 \u00a0 Quebec, Canada","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047013969","display_name":"Sudhir P. Mudur","orcid":"https://orcid.org/0000-0003-4837-0118"},"institutions":[{"id":"https://openalex.org/I60158472","display_name":"Concordia University","ror":"https://ror.org/0420zvk78","country_code":"CA","type":"education","lineage":["https://openalex.org/I60158472"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Sudhir Mudur","raw_affiliation_strings":["Department of Computer Science, Concordia University 3 \u00a0 3 \u00a0 \u00a0 Montreal, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Concordia University 3 \u00a0 3 \u00a0 \u00a0 Montreal, Canada","institution_ids":["https://openalex.org/I60158472"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5078014032"],"corresponding_institution_ids":["https://openalex.org/I1341412227"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2724,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.5893305,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"23","issue":"1","first_page":"99","last_page":"106"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9745000004768372,"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":0.9745000004768372,"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/T10481","display_name":"Computer Graphics and Visualization Techniques","score":0.9171000123023987,"subfield":{"id":"https://openalex.org/subfields/1704","display_name":"Computer Graphics and Computer-Aided Design"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.9065999984741211,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/computer-science","display_name":"Computer science","score":0.6802030801773071},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6618603467941284},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"Energy landscape","score":0.5835967063903809},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.571255624294281},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.4607694149017334},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3325243890285492},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1728949248790741}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6802030801773071},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6618603467941284},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.5835967063903809},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.571255624294281},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4607694149017334},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3325243890285492},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1728949248790741},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D050052","descriptor_name":"TRPC Cation Channels","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D050052","descriptor_name":"TRPC Cation Channels","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D050052","descriptor_name":"TRPC Cation Channels","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btl538","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl538","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/1/99/49816261/bioinformatics_23_1_99.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17062588","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17062588","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.128.1107","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.128.1107","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/btl538v1.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl538","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl538","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/1/99/49816261/bioinformatics_23_1_99.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2154237723.pdf","grobid_xml":"https://content.openalex.org/works/W2154237723.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1500047064","https://openalex.org/W1658649599","https://openalex.org/W1960408443","https://openalex.org/W1981011880","https://openalex.org/W1990606222","https://openalex.org/W1992422451","https://openalex.org/W1996518756","https://openalex.org/W2018312454","https://openalex.org/W2032008622","https://openalex.org/W2034469541","https://openalex.org/W2040809566","https://openalex.org/W2042490093","https://openalex.org/W2046379303","https://openalex.org/W2047510784","https://openalex.org/W2047730466","https://openalex.org/W2069288013","https://openalex.org/W2078889580","https://openalex.org/W2095911937","https://openalex.org/W2104414143","https://openalex.org/W2135469866","https://openalex.org/W2141018272","https://openalex.org/W2142578757","https://openalex.org/W2155512447","https://openalex.org/W2159923313","https://openalex.org/W4206643032","https://openalex.org/W6681104111"],"related_works":["https://openalex.org/W2186061937","https://openalex.org/W2980640053","https://openalex.org/W789507602","https://openalex.org/W2789914061","https://openalex.org/W1649895068","https://openalex.org/W2113188411","https://openalex.org/W1974862140","https://openalex.org/W2049509393","https://openalex.org/W4252654006","https://openalex.org/W2467603891"],"abstract_inverted_index":{"The":[0,77],"mechanism":[1,27],"of":[2,45,50,71,73,91],"protein":[3,25,82,99,156,173],"folding":[4,26,66,83,174],"remains":[5],"largely":[6],"a":[7,116,151,154],"mystery":[8],"in":[9,19,94,104],"molecular":[10],"biology,":[11],"despite":[12],"the":[13,20,24,33,43,48,65,98,101,105,112,135,140],"enormous":[14],"effort":[15],"from":[16],"many":[17],"groups":[18],"past":[21],"decades.":[22],"Currently,":[23],"is":[28],"often":[29],"characterized":[30],"by":[31],"calculating":[32],"free":[34],"energy":[35],"landscape":[36,103],"versus":[37],"various":[38],"reaction":[39,75],"coordinates":[40],"such":[41],"as":[42,97],"fraction":[44],"native":[46],"contacts,":[47],"radius":[49],"gyration":[51],"and":[52,88,137,153,166,176],"so":[53],"on.":[54],"In":[55],"this":[56,121,162],"paper,":[57],"we":[58,118,158],"present":[59,125],"an":[60,126],"integrated":[61],"approach":[62,168],"towards":[63],"understanding":[64],"process":[67],"via":[68,111],"visual":[69],"analysis":[70],"patterns":[72,136],"these":[74],"coordinates.":[76],"three":[78],"disparate":[79],"processes":[80],"(1)":[81],"simulation,":[84],"(2)":[85],"pattern":[86,106,130,164],"elicitation":[87],"(3)":[89],"visualization":[90,113,144,167],"patterns,":[92],"work":[93],"tandem.":[95],"Thus":[96],"folds,":[100],"changing":[102],"space":[107],"can":[108],"be":[109],"viewed":[110],"tool,":[114],"PROTERAN,":[115],"program":[117],"developed":[119],"for":[120],"purpose.":[122],"We":[123],"first":[124],"incremental":[127],"(on-line)":[128],"trie-based":[129],"discovery":[131,165],"algorithm":[132],"to":[133],"elicit":[134],"then":[138],"describe":[139],"terrain":[141],"metaphor":[142],"based":[143],"tool.":[145],"Using":[146],"two":[147],"example":[148],"small":[149],"proteins,":[150],"beta-hairpin":[152],"designed":[155],"Trp-cage,":[157],"next":[159],"demonstrate":[160],"that":[161],"combined":[163],"extracts":[169],"crucial":[170],"information":[171],"about":[172],"intermediates":[175],"mechanism.":[177]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
