{"id":"https://openalex.org/W2021765900","doi":"https://doi.org/10.1177/0278364908098092","title":"Residue Level Three-dimensional Workspace Maps for Conformational Trajectory Planning of Proteins","display_name":"Residue Level Three-dimensional Workspace Maps for Conformational Trajectory Planning of Proteins","publication_year":2009,"publication_date":"2009-03-18","ids":{"openalex":"https://openalex.org/W2021765900","doi":"https://doi.org/10.1177/0278364908098092","mag":"2021765900"},"language":"en","primary_location":{"id":"doi:10.1177/0278364908098092","is_oa":false,"landing_page_url":"https://doi.org/10.1177/0278364908098092","pdf_url":null,"source":{"id":"https://openalex.org/S73484101","display_name":"The International Journal of Robotics Research","issn_l":"0278-3649","issn":["0278-3649","1741-3176"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of Robotics Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5009228712","display_name":"Christopher Madden","orcid":"https://orcid.org/0000-0001-9194-4143"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Madden","raw_affiliation_strings":["Department of Mechanical Engineering, University of Connecticut, USA","Department of Mechanical Engineering, University of Connecticut, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, University of Connecticut, USA","institution_ids":["https://openalex.org/I140172145"]},{"raw_affiliation_string":"Department of Mechanical Engineering, University of Connecticut, USA,","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006450665","display_name":"Peter Bohnenkamp","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter Bohnenkamp","raw_affiliation_strings":["Department of Mechanical Engineering, University of Connecticut, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, University of Connecticut, USA,","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064791506","display_name":"Kazem Kazerounian","orcid":"https://orcid.org/0009-0004-7115-0070"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kazem Kazerounian","raw_affiliation_strings":["Department of Mechanical Engineering, University of Connecticut, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, University of Connecticut, USA,","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103078565","display_name":"Horea Ilie\u015f","orcid":"https://orcid.org/0009-0000-1038-4536"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Horea T. Ilie\u015f","raw_affiliation_strings":["Department of Mechanical Engineering, University of Connecticut, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, University of Connecticut, USA,","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5006450665","https://openalex.org/A5064791506","https://openalex.org/A5103078565"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":null,"apc_paid":null,"fwci":0.546,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.66248719,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"28","issue":"4","first_page":"450","last_page":"463"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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/T10044","display_name":"Protein Structure and Dynamics","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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T11162","display_name":"Enzyme Structure and Function","score":0.9944000244140625,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/workspace","display_name":"Workspace","score":0.7552483081817627},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.6883788108825684},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.6866317391395569},{"id":"https://openalex.org/keywords/cartesian-coordinate-system","display_name":"Cartesian coordinate system","score":0.6552397012710571},{"id":"https://openalex.org/keywords/euclidean-space","display_name":"Euclidean space","score":0.5980254411697388},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5237724184989929},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5178242325782776},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5023641586303711},{"id":"https://openalex.org/keywords/euclidean-geometry","display_name":"Euclidean geometry","score":0.4841535687446594},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.4559820294380188},{"id":"https://openalex.org/keywords/euclidean-distance","display_name":"Euclidean distance","score":0.44985896348953247},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4164985418319702},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33205801248550415},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27886396646499634},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2788635492324829},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.22602248191833496},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.19470179080963135},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.193389892578125},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.1803133487701416},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.17091625928878784},{"id":"https://openalex.org/keywords/robot","display_name":"Robot","score":0.12235701084136963},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0975002646446228}],"concepts":[{"id":"https://openalex.org/C58581272","wikidata":"https://www.wikidata.org/wiki/Q12741163","display_name":"Workspace","level":3,"score":0.7552483081817627},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.6883788108825684},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.6866317391395569},{"id":"https://openalex.org/C16038011","wikidata":"https://www.wikidata.org/wiki/Q62912","display_name":"Cartesian coordinate system","level":2,"score":0.6552397012710571},{"id":"https://openalex.org/C186450821","wikidata":"https://www.wikidata.org/wiki/Q17295","display_name":"Euclidean space","level":2,"score":0.5980254411697388},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5237724184989929},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5178242325782776},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5023641586303711},{"id":"https://openalex.org/C129782007","wikidata":"https://www.wikidata.org/wiki/Q162886","display_name":"Euclidean geometry","level":2,"score":0.4841535687446594},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4559820294380188},{"id":"https://openalex.org/C120174047","wikidata":"https://www.wikidata.org/wiki/Q847073","display_name":"Euclidean distance","level":2,"score":0.44985896348953247},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4164985418319702},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33205801248550415},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27886396646499634},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2788635492324829},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.22602248191833496},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.19470179080963135},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.193389892578125},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.1803133487701416},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.17091625928878784},{"id":"https://openalex.org/C90509273","wikidata":"https://www.wikidata.org/wiki/Q11012","display_name":"Robot","level":2,"score":0.12235701084136963},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0975002646446228},{"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/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1177/0278364908098092","is_oa":false,"landing_page_url":"https://doi.org/10.1177/0278364908098092","pdf_url":null,"source":{"id":"https://openalex.org/S73484101","display_name":"The International Journal of Robotics Research","issn_l":"0278-3649","issn":["0278-3649","1741-3176"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of Robotics Research","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/11","display_name":"Sustainable cities and communities","score":0.5600000023841858}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W102175168","https://openalex.org/W1846743956","https://openalex.org/W1966299504","https://openalex.org/W1969723894","https://openalex.org/W1984546173","https://openalex.org/W2026258231","https://openalex.org/W2030866185","https://openalex.org/W2043528001","https://openalex.org/W2046408940","https://openalex.org/W2047544230","https://openalex.org/W2049526049","https://openalex.org/W2049598343","https://openalex.org/W2049902088","https://openalex.org/W2050595677","https://openalex.org/W2052581033","https://openalex.org/W2061258525","https://openalex.org/W2061629466","https://openalex.org/W2064139541","https://openalex.org/W2069123478","https://openalex.org/W2073839370","https://openalex.org/W2075409132","https://openalex.org/W2082462938","https://openalex.org/W2105254477","https://openalex.org/W2108700551","https://openalex.org/W2111717302","https://openalex.org/W2122199548","https://openalex.org/W2125380479","https://openalex.org/W2126162505","https://openalex.org/W2127650328","https://openalex.org/W2140889378","https://openalex.org/W2153131823","https://openalex.org/W2154535641","https://openalex.org/W2165108031","https://openalex.org/W2168989513","https://openalex.org/W4249658256","https://openalex.org/W4392468778"],"related_works":["https://openalex.org/W2020669016","https://openalex.org/W2088162897","https://openalex.org/W2090630809","https://openalex.org/W4387804157","https://openalex.org/W2106612397","https://openalex.org/W2518314460","https://openalex.org/W2401430279","https://openalex.org/W2119891507","https://openalex.org/W2089869950","https://openalex.org/W2589205199"],"abstract_inverted_index":{"The":[0],"function":[1],"of":[2,22,46,66,69,81],"a":[3,44,78,141],"protein":[4,53,70,193],"macromolecule":[5],"often":[6],"requires":[7],"conformational":[8],"transitions":[9,16],"between":[10,144],"two":[11,163],"native":[12],"conformations.":[13,197],"Understanding":[14],"these":[15],"is":[17,134,140,191],"essential":[18],"to":[19,29,32,76,173],"the":[20,30,61,97,105,116,121,127,135,145,151,155,162,166,170,178,187],"understanding":[21],"how":[23],"proteins":[24,86,95],"function,":[25],"as":[26,28],"well":[27],"ability":[31],"design":[33],"and":[34,150],"manipulate":[35],"protein-based":[36],"nanomechanical":[37],"systems.":[38],"In":[39],"this":[40,131],"paper":[41],"we":[42],"propose":[43],"set":[45],"3D":[47,56,107,152,167,179],"Cartesian":[48,153],"workspace":[49],"maps":[50,57,109,118,149,168],"for":[51,64,130],"exploring":[52],"pathways.":[54],"These":[55],"are":[58,110,158],"constructed":[59,119],"in":[60,83,120,161,177,186],"Euclidean":[62,180],"space":[63,181],"triads":[65],"chain":[67],"segments":[68],"molecules":[71,194],"that":[72,104,126],"have":[73,77],"been":[74],"shown":[75],"high":[79],"probability":[80],"occurrence":[82],"naturally":[84],"observed":[85],"based":[87,182],"on":[88,183],"data":[89],"obtained":[90],"from":[91,96],"more":[92,111],"than":[93,115],"38,600":[94],"Protein":[98],"Data":[99],"Bank":[100],"(PDB).":[101],"We":[102,124],"show":[103],"proposed":[106],"propensity":[108,117,156],"effective":[112],"navigation":[113],"tools":[114],"angle":[122,148],"space.":[123],"argue":[125],"main":[128],"reason":[129],"improved":[132],"efficiency":[133],"fact":[136],"that,":[137],"although":[138],"there":[139],"one-to-one":[142],"mapping":[143],"2D":[146],"dihedral":[147],"maps,":[154],"distributions":[157],"significantly":[159],"different":[160],"spaces.":[164],"Hence,":[165],"allow":[169],"pathway":[171],"planning":[172],"be":[174],"performed":[175],"directly":[176],"propensities":[184],"computed":[185],"same":[188],"space,":[189],"which":[190],"where":[192],"change":[195],"their":[196]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-03T06:03:33.228499","created_date":"2025-10-10T00:00:00"}
