{"id":"https://openalex.org/W4212911575","doi":"https://doi.org/10.1002/1097-0134(20010101)42:1<6::aid-prot20>3.3.co;2-z","title":"Modeling the third loop of short\u2010chain snake venom neurotoxins: Roles of the short\u2010range and long\u2010range interactions","display_name":"Modeling the third loop of short\u2010chain snake venom neurotoxins: Roles of the short\u2010range and long\u2010range interactions","publication_year":2001,"publication_date":"2001-01-01","ids":{"openalex":"https://openalex.org/W4212911575","doi":"https://doi.org/10.1002/1097-0134(20010101)42:1<6::aid-prot20>3.3.co;2-z"},"language":"en","primary_location":{"id":"doi:10.1002/1097-0134(20010101)42:1<6::aid-prot20>3.3.co;2-z","doi":"https://doi.org/10.1002/1097-0134(20010101)42:1<6::aid-prot20>3.3.co;2-z","is_oa":false,"landing_page_url":"https://doi.org/10.1002/1097-0134(20010101)42:1<6::aid-prot20>3.3.co;2-z","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Genetics","raw_type":"journal-article"},"volume":null,"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":null,"display_name":"Zhijie Liu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhijie Liu","raw_affiliation_strings":["Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391768210"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027145422","display_name":"Weizhong Li","orcid":"https://orcid.org/0000-0003-1804-9403","observed_orcids":["https://orcid.org/0000-0003-1804-9403"]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weizhong Li","raw_affiliation_strings":["Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391768210"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100412608","display_name":"Hongyu Zhang","orcid":"https://orcid.org/0000-0002-8078-4401","observed_orcids":["https://orcid.org/0000-0002-8078-4401","https://orcid.org/0009-0006-6503-9442"]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongyu Zhang","raw_affiliation_strings":["Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391768210"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101689212","display_name":"Yuzhen Han","orcid":"https://orcid.org/0000-0003-3330-1902","observed_orcids":["https://orcid.org/0000-0003-3330-1902"]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuzhen Han","raw_affiliation_strings":["Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391768210"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064049271","display_name":"Luhua Lai","orcid":"https://orcid.org/0000-0002-8343-7587","observed_orcids":["https://orcid.org/0000-0002-8343-7587"]},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Luhua Lai","raw_affiliation_strings":["Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry & College of Chemistry and Molecular Engineering, Peking University, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing, P.R. China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391768210"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5064049271"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4391768210"],"apc_list":{"value":4550,"currency":"USD","value_usd":4550},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.3066787,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"42","issue":"1","first_page":"6","last_page":"16"},"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/T11353","display_name":"Venomous Animal Envenomation and Studies","score":0.0013000000035390258,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.0003000000142492354,"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/snake-neurotoxins","display_name":"snake venom neurotoxins","score":0.9459999799728394},{"id":"https://openalex.org/keywords/erabutoxin-b","display_name":"erabutoxin b","score":0.878000020980835},{"id":"https://openalex.org/keywords/long-range-interactions","display_name":"long-range interactions","score":0.8510000109672546},{"id":"https://openalex.org/keywords/short-range-interactions","display_name":"short-range interactions","score":0.9290000200271606},{"id":"https://openalex.org/keywords/beta-turn","display_name":"beta-turn","score":0.43299999833106995},{"id":"https://openalex.org/keywords/type-ii-beta-turn","display_name":"type II beta-turn","score":0.9240000247955322},{"id":"https://openalex.org/keywords/surface-loops","display_name":"surface loops","score":0.5220000147819519},{"id":"https://openalex.org/keywords/protein-folding","display_name":"protein folding","score":0.5849999785423279},{"id":"https://openalex.org/keywords/monte-carlo-simulated-annealing","display_name":"Monte Carlo simulated annealing","score":0.7699999809265137}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5601041316986084},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5226378440856934},{"id":"https://openalex.org/C85641259","wikidata":"https://www.wikidata.org/wiki/Q290042","display_name":"Turn (biochemistry)","level":2,"score":0.5177411437034607},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5060600638389587},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.48288679122924805},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4783487021923065},{"id":"https://openalex.org/C19472624","wikidata":"https://www.wikidata.org/wiki/Q583851","display_name":"Native state","level":2,"score":0.4739534854888916},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.46511390805244446},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.46157750487327576},{"id":"https://openalex.org/C2776725428","wikidata":"https://www.wikidata.org/wiki/Q424200","display_name":"Snake venom","level":3,"score":0.4589986801147461},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.44357407093048096},{"id":"https://openalex.org/C206276672","wikidata":"https://www.wikidata.org/wiki/Q5164839","display_name":"Contact order","level":3,"score":0.43892142176628113},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.42980003356933594},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.428079754114151},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.42424729466438293},{"id":"https://openalex.org/C2779448229","wikidata":"https://www.wikidata.org/wiki/Q3386847","display_name":"Venom","level":2,"score":0.41358470916748047},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.25650012493133545},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2145146131515503},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1874222457408905},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.12629976868629456},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"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/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/1097-0134(20010101)42:1<6::aid-prot20>3.3.co;2-z","doi":"https://doi.org/10.1002/1097-0134(20010101)42:1<6::aid-prot20>3.3.co;2-z","is_oa":false,"landing_page_url":"https://doi.org/10.1002/1097-0134(20010101)42:1<6::aid-prot20>3.3.co;2-z","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Genetics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2120160533","https://openalex.org/W2082472404","https://openalex.org/W2087715078","https://openalex.org/W2366295031","https://openalex.org/W2049307663","https://openalex.org/W2056429570","https://openalex.org/W4248361876","https://openalex.org/W2341750030","https://openalex.org/W2333096563","https://openalex.org/W2019423777"],"abstract_inverted_index":{"The":[0,67],"influence":[1],"of":[2,36,46,48,94,160],"long-range":[3,150,184],"interactions":[4,151,170,185],"on":[5],"local":[6],"structures":[7],"is":[8],"an":[9],"important":[10],"issue":[11],"in":[12,43,58,76,91,125,138,166],"understanding":[13],"protein":[14,18,69,127,140],"folding":[15],"process":[16],"and":[17,105,113,157],"structure":[19,70],"stability.":[20],"Using":[21,129],"short-chain":[22,50],"snake":[23],"venom":[24],"neurotoxin":[25],"as":[26],"a":[27,163],"model":[28],"system,":[29],"we":[30],"have":[31,178],"studied":[32],"the":[33,44,49,78,83,106,126,134,139,144,155,158,183],"conformational":[34,136],"properties":[35],"eight":[37,84],"different":[38],"loop":[39,79,165],"III":[40],"sequences":[41],"either":[42],"environment":[45,141],"one":[47],"neurotoxin,":[51],"erabutoxin":[52],"b":[53],"(PDB":[54],"ID":[55],"1nxb),":[56],"or":[57],"free":[59],"state":[60],"by":[61,182],"Monte":[62],"Carlo":[63],"simulated":[64],"annealing":[65],"method.":[66],"surrounding":[68],"was":[71],"found":[72],"to":[73,100,117,132,154,179],"be":[74,180],"crucial":[75],"stabilizing":[77],"conformation.":[80],"Although":[81],"all":[82],"peptides":[85],"prefer":[86],"type":[87,101,120],"V":[88,121],"\u03b2":[89,103,122],"turn":[90,99,104,123],"solution,":[92],"three":[93],"them":[95],"(KPGI,":[96],"KPGV,":[97],"KSGI)":[98],"II":[102],"other":[107],"five":[108],"(KKGI,":[109],"KKGV,":[110],"KNGI,":[111],"KQGI,":[112],"KRGV)":[114],"are":[115],"confined":[116],"more":[118],"rigid":[119],"conformation":[124,161],"structure.":[128],"flexible":[130],"tetra-glycine-peptide":[131],"screen":[133],"backbone":[135],"space":[137],"also":[142],"validates":[143],"results.":[145],"This":[146],"study":[147],"shows":[148],"that":[149],"do":[152],"contribute":[153],"stability":[156],"types":[159],"for":[162],"surface":[164],"protein,":[167],"while":[168],"short-range":[169],"may":[171],"only":[172],"provide":[173],"candidate":[174],"conformations,":[175],"which":[176],"then":[177],"filtered":[181],"further.":[186],"Proteins":[187],"2001;42:6\u201316.":[188],"\u00a9":[189],"2000":[190],"Wiley-Liss,":[191],"Inc.":[192]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-10-27T15:51:10.671819","created_date":"2022-02-24T00:00:00"}
