{"id":"https://openalex.org/W2160028263","doi":"https://doi.org/10.1093/bioinformatics/btl325","title":"Prediction and simulation of motion in pairs of transmembrane \u03b1-helices","display_name":"Prediction and simulation of motion in pairs of transmembrane \u03b1-helices","publication_year":2007,"publication_date":"2007-01-15","ids":{"openalex":"https://openalex.org/W2160028263","doi":"https://doi.org/10.1093/bioinformatics/btl325","mag":"2160028263"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl325","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl325","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/2/e212/49820628/bioinformatics_23_2_e212.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"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/23/2/e212/49820628/bioinformatics_23_2_e212.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025089277","display_name":"Angela Enosh","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Angela Enosh","raw_affiliation_strings":["School of Computer Science 1 \u00a0 1 \u00a0 \u00a0 Ramat Aviv 69978, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science 1 \u00a0 1 \u00a0 \u00a0 Ramat Aviv 69978, Israel","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031768744","display_name":"Sarel J. Fleishman","orcid":"https://orcid.org/0000-0003-3177-7560"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Sarel J. Fleishman","raw_affiliation_strings":["Department of Biochemistry Tel Aviv University 2 \u00a0 2 \u00a0 \u00a0 Ramat Aviv 69978, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry Tel Aviv University 2 \u00a0 2 \u00a0 \u00a0 Ramat Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037671858","display_name":"Nir Ben\u2010Tal","orcid":"https://orcid.org/0000-0001-6901-832X"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Nir Ben-Tal","raw_affiliation_strings":["Department of Biochemistry Tel Aviv University 2 \u00a0 2 \u00a0 \u00a0 Ramat Aviv 69978, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry Tel Aviv University 2 \u00a0 2 \u00a0 \u00a0 Ramat Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038503253","display_name":"Dan Halperin","orcid":"https://orcid.org/0000-0002-3345-3765"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dan Halperin","raw_affiliation_strings":["School of Computer Science 1 \u00a0 1 \u00a0 \u00a0 Ramat Aviv 69978, Israel"],"affiliations":[{"raw_affiliation_string":"School of Computer Science 1 \u00a0 1 \u00a0 \u00a0 Ramat Aviv 69978, Israel","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025089277"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8325,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.85054355,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"23","issue":"2","first_page":"e212","last_page":"e218"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9957000017166138,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9957000017166138,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9771000146865845,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9757999777793884,"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/motion","display_name":"Motion (physics)","score":0.5777852535247803},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5755106806755066},{"id":"https://openalex.org/keywords/glycophorin","display_name":"Glycophorin","score":0.5564810037612915},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.5016303062438965},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.5010106563568115},{"id":"https://openalex.org/keywords/degrees-of-freedom","display_name":"Degrees of freedom (physics and chemistry)","score":0.4775586724281311},{"id":"https://openalex.org/keywords/transmembrane-domain","display_name":"Transmembrane domain","score":0.4351702630519867},{"id":"https://openalex.org/keywords/transmembrane-protein","display_name":"Transmembrane protein","score":0.43111446499824524},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.41876888275146484},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4006902873516083},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3963259756565094},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.24642512202262878},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17875167727470398},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11202412843704224},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11059620976448059}],"concepts":[{"id":"https://openalex.org/C104114177","wikidata":"https://www.wikidata.org/wiki/Q79782","display_name":"Motion (physics)","level":2,"score":0.5777852535247803},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5755106806755066},{"id":"https://openalex.org/C67982717","wikidata":"https://www.wikidata.org/wiki/Q24724397","display_name":"Glycophorin","level":3,"score":0.5564810037612915},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.5016303062438965},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.5010106563568115},{"id":"https://openalex.org/C208081375","wikidata":"https://www.wikidata.org/wiki/Q274502","display_name":"Degrees of freedom (physics and chemistry)","level":2,"score":0.4775586724281311},{"id":"https://openalex.org/C118892022","wikidata":"https://www.wikidata.org/wiki/Q7834587","display_name":"Transmembrane domain","level":3,"score":0.4351702630519867},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.43111446499824524},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.41876888275146484},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4006902873516083},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3963259756565094},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.24642512202262878},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17875167727470398},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11202412843704224},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11059620976448059},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btl325","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl325","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/2/e212/49820628/bioinformatics_23_2_e212.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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl325","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl325","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/2/e212/49820628/bioinformatics_23_2_e212.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":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320319059","display_name":"Clore Israel Foundation","ror":"https://ror.org/00mmfdg02"},{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320322596","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160028263.pdf","grobid_xml":"https://content.openalex.org/works/W2160028263.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W101508493","https://openalex.org/W1424654272","https://openalex.org/W1521785144","https://openalex.org/W1653812874","https://openalex.org/W1722544174","https://openalex.org/W1820924839","https://openalex.org/W1844162177","https://openalex.org/W1977708375","https://openalex.org/W2002948689","https://openalex.org/W2015403140","https://openalex.org/W2025786614","https://openalex.org/W2028702957","https://openalex.org/W2033488181","https://openalex.org/W2034626992","https://openalex.org/W2037644310","https://openalex.org/W2037907469","https://openalex.org/W2047163848","https://openalex.org/W2067763399","https://openalex.org/W2074362388","https://openalex.org/W2077228745","https://openalex.org/W2081030911","https://openalex.org/W2093221728","https://openalex.org/W2099384461","https://openalex.org/W2115257338","https://openalex.org/W2116349394","https://openalex.org/W2126162505","https://openalex.org/W2128990851","https://openalex.org/W2131850891","https://openalex.org/W2139230981","https://openalex.org/W2171266831","https://openalex.org/W2611243847","https://openalex.org/W2645793119","https://openalex.org/W3022388728","https://openalex.org/W3104753760","https://openalex.org/W4242811155","https://openalex.org/W4252017042","https://openalex.org/W6636918919","https://openalex.org/W6637841280","https://openalex.org/W6638575927","https://openalex.org/W6638984643"],"related_works":["https://openalex.org/W3099772455","https://openalex.org/W3172198228","https://openalex.org/W1986078734","https://openalex.org/W2129301794","https://openalex.org/W1963755507","https://openalex.org/W1977095816","https://openalex.org/W60395508","https://openalex.org/W2020478092","https://openalex.org/W2063247848","https://openalex.org/W1991442277"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Motion":[2],"in":[3,11,27,34,54,105,114,131,171,230,253],"transmembrane":[4],"(TM)":[5],"proteins":[6,31,56],"plays":[7],"an":[8,19,35,47],"essential":[9],"role":[10],"a":[12,96,132,158,173,179,237],"variety":[13,174],"of":[14,30,38,40,57,83,99,101,121,143,165,175,185,199,248],"biological":[15],"phenomena.":[16],"Thus,":[17],"developing":[18],"automated":[20],"method":[21,63],"for":[22,49,182],"predicting":[23,50],"and":[24,51,110,155,202,221],"simulating":[25,52],"motion":[26,53,72,142,210],"this":[28,200,207,227,249],"class":[29],"should":[32],"result":[33],"increased":[36],"level":[37],"understanding":[39],"crucial":[41],"physiological":[42],"mechanisms.":[43],"We":[44,190],"have":[45],"developed":[46],"algorithm":[48,94,147,193],"TM":[55,91,197,250],"the":[58,81,84,90,106,118,122,140,144,149,153,166,186,196,216,246],"\u03b1-helix":[59],"bundle":[60],"type.":[61],"Our":[62,93,146,243],"employs":[64],"probabilistic":[65],"motion-planning":[66],"techniques":[67],"to":[68,80,116,137,194,215,226],"suggest":[69],"possible":[70],"collision-free":[71],"paths.":[73],"The":[74],"resulting":[75,252],"paths":[76,255],"are":[77,263],"ranked":[78,219],"according":[79],"quality":[82],"van":[85],"der":[86],"Waals":[87],"interactions":[88],"between":[89],"helices.":[92],"considers":[95],"wide":[97],"range":[98],"degrees":[100],"freedom":[102],"(dofs)":[103],"involved":[104],"motion,":[107,150],"including":[108,151],"external":[109],"internal":[111],"moves.":[112],"However,":[113],"order":[115],"handle":[117],"vast":[119],"dimensionality":[120],"problem,":[123],"we":[124,235],"employ":[125],"some":[126],"constraints":[127],"on":[128],"these":[129],"dofs":[130],"way":[133],"that":[134,160,212],"is":[135],"unlikely":[136],"rule":[138],"out":[139],"native":[141],"protein.":[145],"simulates":[148],"all":[152],"dofs,":[154],"automatically":[156],"produces":[157],"movie":[159],"demonstrates":[161],"it.":[162],"Results:":[163],"Overexpression":[164],"RTK":[167],"ErbB2":[168],"was":[169,188,213],"implicated":[170],"causing":[172],"human":[176],"cancers.":[177],"Recently,":[178],"molecular":[180],"mechanism":[181,218],"rotation-coupled":[183],"activation":[184],"receptor":[187],"suggested.":[189],"applied":[191],"our":[192,204],"investigate":[195],"domain":[198],"protein,":[201,251],"compared":[203],"results":[205,244],"with":[206,223],"mechanism.":[208],"A":[209],"pathway":[211,228],"similar":[214],"proposed":[217],"first,":[220],"motions":[222],"partial":[224],"overlap":[225],"followed":[229],"rank":[231],"order.":[232],"In":[233],"addition,":[234],"conducted":[236],"negative-control":[238],"computational-experiment":[239],"using":[240],"Glycophorin":[241],"A.":[242],"confirmed":[245],"immobility":[247],"degenerate":[254],"comprising":[256],"native-like":[257],"conformations.":[258],"Supplementary":[259,261],"information:":[260],"data":[262],"available":[264],"at":[265],"Contact:":[266],"angela@post.tau.ac.il":[267]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
