{"id":"https://openalex.org/W2060989213","doi":"https://doi.org/10.1007/s10822-012-9588-4","title":"Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules","display_name":"Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules","publication_year":2012,"publication_date":"2012-07-24","ids":{"openalex":"https://openalex.org/W2060989213","doi":"https://doi.org/10.1007/s10822-012-9588-4","mag":"2060989213","pmid":"https://pubmed.ncbi.nlm.nih.gov/22829296"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-012-9588-4","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-012-9588-4","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"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/A5023681675","display_name":"Liang Xu","orcid":"https://orcid.org/0000-0002-6556-7521"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Liang Xu","raw_affiliation_strings":["School of Chemistry, Dalian University of Technology, Dalian, China. xuliang@dlut.edu.cn","[School of Chemistry, Dalian University of Technology, Dalian, China]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chemistry, Dalian University of Technology, Dalian, China. xuliang@dlut.edu.cn","institution_ids":["https://openalex.org/I27357992","https://openalex.org/I4210092944"]},{"raw_affiliation_string":"[School of Chemistry, Dalian University of Technology, Dalian, China]","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011881217","display_name":"Ke Gao","orcid":"https://orcid.org/0000-0002-7011-1529"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ke Gao","raw_affiliation_strings":["School of Chemistry, Dalian University of Technology, Dalian, 116024, China","Dalian Univ of Tech"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chemistry, Dalian University of Technology, Dalian, 116024, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"Dalian Univ of Tech","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104046393","display_name":"Chunyu Bao","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chunyu Bao","raw_affiliation_strings":["School of Chemistry, Dalian University of Technology, Dalian, 116024, China","Dalian Univ of Tech"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chemistry, Dalian University of Technology, Dalian, 116024, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"Dalian Univ of Tech","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101894836","display_name":"Xicheng Wang","orcid":"https://orcid.org/0000-0002-2719-2538"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xicheng Wang","raw_affiliation_strings":["Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian, 116023, China","Dalian Univ of Tech"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian, 116023, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"Dalian Univ of Tech","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5023681675"],"corresponding_institution_ids":["https://openalex.org/I27357992","https://openalex.org/I4210092944"],"apc_list":{"value":3690,"currency":"USD","value_usd":3690},"apc_paid":null,"fwci":1.9419,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.86404485,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"26","issue":"8","first_page":"963","last_page":"976"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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/T10086","display_name":"Alzheimer's disease research and treatments","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bifunctional","display_name":"Bifunctional","score":0.9352083206176758},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.7770252227783203},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.5871365070343018},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5441895127296448},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.518337607383728},{"id":"https://openalex.org/keywords/umbrella-sampling","display_name":"Umbrella sampling","score":0.5027010440826416},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.34805023670196533},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3280488848686218},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.29963767528533936},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14653080701828003},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.08152887225151062}],"concepts":[{"id":"https://openalex.org/C2780443040","wikidata":"https://www.wikidata.org/wiki/Q3737863","display_name":"Bifunctional","level":3,"score":0.9352083206176758},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7770252227783203},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5871365070343018},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5441895127296448},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.518337607383728},{"id":"https://openalex.org/C128747166","wikidata":"https://www.wikidata.org/wiki/Q7881414","display_name":"Umbrella sampling","level":3,"score":0.5027010440826416},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.34805023670196533},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3280488848686218},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.29963767528533936},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14653080701828003},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08152887225151062},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000544","descriptor_name":"Alzheimer Disease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000544","descriptor_name":"Alzheimer Disease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000544","descriptor_name":"Alzheimer Disease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-012-9588-4","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-012-9588-4","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:22829296","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22829296","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":"Journal of computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.75}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":96,"referenced_works":["https://openalex.org/W77683630","https://openalex.org/W134536487","https://openalex.org/W1595368494","https://openalex.org/W1677883125","https://openalex.org/W1707143272","https://openalex.org/W1838272947","https://openalex.org/W1935356375","https://openalex.org/W1963591142","https://openalex.org/W1965893983","https://openalex.org/W1968041782","https://openalex.org/W1974479642","https://openalex.org/W1974643980","https://openalex.org/W1975580333","https://openalex.org/W1976499671","https://openalex.org/W1976544813","https://openalex.org/W1978918572","https://openalex.org/W1980709154","https://openalex.org/W1984155407","https://openalex.org/W1984552405","https://openalex.org/W1984964811","https://openalex.org/W1996037698","https://openalex.org/W2002754698","https://openalex.org/W2003223057","https://openalex.org/W2004605168","https://openalex.org/W2006280602","https://openalex.org/W2008151389","https://openalex.org/W2009527674","https://openalex.org/W2010076108","https://openalex.org/W2011056613","https://openalex.org/W2011666658","https://openalex.org/W2011810121","https://openalex.org/W2012363870","https://openalex.org/W2012671084","https://openalex.org/W2015688756","https://openalex.org/W2017578362","https://openalex.org/W2021989110","https://openalex.org/W2022325790","https://openalex.org/W2025200427","https://openalex.org/W2027123848","https://openalex.org/W2032881767","https://openalex.org/W2035963355","https://openalex.org/W2037953319","https://openalex.org/W2040650067","https://openalex.org/W2040809566","https://openalex.org/W2041230020","https://openalex.org/W2041499235","https://openalex.org/W2042726738","https://openalex.org/W2045288389","https://openalex.org/W2051609969","https://openalex.org/W2052046119","https://openalex.org/W2059462172","https://openalex.org/W2060409666","https://openalex.org/W2062820102","https://openalex.org/W2063679630","https://openalex.org/W2065100984","https://openalex.org/W2066962978","https://openalex.org/W2067174909","https://openalex.org/W2070377130","https://openalex.org/W2072467039","https://openalex.org/W2075420978","https://openalex.org/W2076189730","https://openalex.org/W2076976809","https://openalex.org/W2079749054","https://openalex.org/W2079991717","https://openalex.org/W2080100823","https://openalex.org/W2082310867","https://openalex.org/W2083164383","https://openalex.org/W2083587135","https://openalex.org/W2084187244","https://openalex.org/W2086142786","https://openalex.org/W2087947213","https://openalex.org/W2095674336","https://openalex.org/W2096410114","https://openalex.org/W2107947409","https://openalex.org/W2114078421","https://openalex.org/W2117285383","https://openalex.org/W2121374178","https://openalex.org/W2122294662","https://openalex.org/W2128572087","https://openalex.org/W2131288855","https://openalex.org/W2133035474","https://openalex.org/W2142632602","https://openalex.org/W2144288821","https://openalex.org/W2147993766","https://openalex.org/W2149302140","https://openalex.org/W2152058429","https://openalex.org/W2153332667","https://openalex.org/W2155779385","https://openalex.org/W2158534713","https://openalex.org/W2163399017","https://openalex.org/W2163552626","https://openalex.org/W2164270482","https://openalex.org/W2165526004","https://openalex.org/W2165779834","https://openalex.org/W2166667985","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2312657253","https://openalex.org/W2343617961","https://openalex.org/W2065583757","https://openalex.org/W2407423735","https://openalex.org/W2952163184","https://openalex.org/W2395122550","https://openalex.org/W2953087550","https://openalex.org/W2066760779","https://openalex.org/W2946934695","https://openalex.org/W2060989213"],"abstract_inverted_index":null,"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":4}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
