{"id":"https://openalex.org/W2078145018","doi":"https://doi.org/10.1021/ci900508k","title":"LowModeMD\u2014Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops","display_name":"LowModeMD\u2014Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops","publication_year":2010,"publication_date":"2010-04-29","ids":{"openalex":"https://openalex.org/W2078145018","doi":"https://doi.org/10.1021/ci900508k","mag":"2078145018","pmid":"https://pubmed.ncbi.nlm.nih.gov/20429574"},"language":"en","primary_location":{"id":"doi:10.1021/ci900508k","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci900508k","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"publisher-specific-oa","license_id":"https://openalex.org/licenses/publisher-specific-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5014765766","display_name":"Paul Labute","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Paul Labute","raw_affiliation_strings":["Chemical Computing Group, Inc., 1010 Sherbrooke St. W., Suite 910, Montreal H3A 2R7, Quebec, Canada"],"affiliations":[{"raw_affiliation_string":"Chemical Computing Group, Inc., 1010 Sherbrooke St. W., Suite 910, Montreal H3A 2R7, Quebec, Canada","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5014765766"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":4.3617,"has_fulltext":false,"cited_by_count":332,"citation_normalized_percentile":{"value":0.95180479,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"50","issue":"5","first_page":"792","last_page":"800"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"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":1.0,"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/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6247602701187134},{"id":"https://openalex.org/keywords/kinetic-energy","display_name":"Kinetic energy","score":0.5967409014701843},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.5745812654495239},{"id":"https://openalex.org/keywords/potential-energy","display_name":"Potential energy","score":0.5163053870201111},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.5054018497467041},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.49410250782966614},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"Energy landscape","score":0.4770231246948242},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.47183850407600403},{"id":"https://openalex.org/keywords/vector-field","display_name":"Vector field","score":0.4703536033630371},{"id":"https://openalex.org/keywords/chebyshev-filter","display_name":"Chebyshev filter","score":0.46108219027519226},{"id":"https://openalex.org/keywords/normal-mode","display_name":"Normal mode","score":0.45484694838523865},{"id":"https://openalex.org/keywords/chebyshev-polynomials","display_name":"Chebyshev polynomials","score":0.42427384853363037},{"id":"https://openalex.org/keywords/boltzmann-constant","display_name":"Boltzmann constant","score":0.41857481002807617},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3838675022125244},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.37792330980300903},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.37353211641311646},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.36566638946533203},{"id":"https://openalex.org/keywords/classical-mechanics","display_name":"Classical mechanics","score":0.3627110421657562},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.30053508281707764},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.2286381721496582},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18910250067710876},{"id":"https://openalex.org/keywords/vibration","display_name":"Vibration","score":0.1890774667263031},{"id":"https://openalex.org/keywords/mechanics","display_name":"Mechanics","score":0.1873682141304016},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.15266183018684387},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.11801213026046753}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6247602701187134},{"id":"https://openalex.org/C135889238","wikidata":"https://www.wikidata.org/wiki/Q46276","display_name":"Kinetic energy","level":2,"score":0.5967409014701843},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.5745812654495239},{"id":"https://openalex.org/C84551667","wikidata":"https://www.wikidata.org/wiki/Q155640","display_name":"Potential energy","level":2,"score":0.5163053870201111},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.5054018497467041},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.49410250782966614},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.4770231246948242},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.47183850407600403},{"id":"https://openalex.org/C91188154","wikidata":"https://www.wikidata.org/wiki/Q186247","display_name":"Vector field","level":2,"score":0.4703536033630371},{"id":"https://openalex.org/C21424316","wikidata":"https://www.wikidata.org/wiki/Q718621","display_name":"Chebyshev filter","level":2,"score":0.46108219027519226},{"id":"https://openalex.org/C32758168","wikidata":"https://www.wikidata.org/wiki/Q900488","display_name":"Normal mode","level":3,"score":0.45484694838523865},{"id":"https://openalex.org/C129785596","wikidata":"https://www.wikidata.org/wiki/Q619511","display_name":"Chebyshev polynomials","level":2,"score":0.42427384853363037},{"id":"https://openalex.org/C35304006","wikidata":"https://www.wikidata.org/wiki/Q5962","display_name":"Boltzmann constant","level":2,"score":0.41857481002807617},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3838675022125244},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.37792330980300903},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.37353211641311646},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.36566638946533203},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.3627110421657562},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.30053508281707764},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.2286381721496582},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18910250067710876},{"id":"https://openalex.org/C198394728","wikidata":"https://www.wikidata.org/wiki/Q3695508","display_name":"Vibration","level":2,"score":0.1890774667263031},{"id":"https://openalex.org/C57879066","wikidata":"https://www.wikidata.org/wiki/Q41217","display_name":"Mechanics","level":1,"score":0.1873682141304016},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.15266183018684387},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.11801213026046753},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002417","descriptor_name":"Cattle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047028","descriptor_name":"Macrocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047028","descriptor_name":"Macrocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047028","descriptor_name":"Macrocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054460","descriptor_name":"rho-Associated Kinases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054460","descriptor_name":"rho-Associated Kinases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054460","descriptor_name":"rho-Associated Kinases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci900508k","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci900508k","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"publisher-specific-oa","license_id":"https://openalex.org/licenses/publisher-specific-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:20429574","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20429574","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8999999761581421,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1529327704","https://openalex.org/W1582520000","https://openalex.org/W1650490230","https://openalex.org/W1973056533","https://openalex.org/W1978705163","https://openalex.org/W1980302104","https://openalex.org/W1987355878","https://openalex.org/W2002755329","https://openalex.org/W2015446226","https://openalex.org/W2017251721","https://openalex.org/W2033014917","https://openalex.org/W2035266068","https://openalex.org/W2037535298","https://openalex.org/W2039485495","https://openalex.org/W2040809566","https://openalex.org/W2041902442","https://openalex.org/W2044623988","https://openalex.org/W2050066735","https://openalex.org/W2065705570","https://openalex.org/W2071527014","https://openalex.org/W2073590531","https://openalex.org/W2093151204","https://openalex.org/W2095026430","https://openalex.org/W2122199548","https://openalex.org/W2134738108","https://openalex.org/W2145928638","https://openalex.org/W2147421370","https://openalex.org/W2156171987","https://openalex.org/W2160907977","https://openalex.org/W2323178299","https://openalex.org/W4234347480","https://openalex.org/W4236316114"],"related_works":["https://openalex.org/W2390710574","https://openalex.org/W2044897135","https://openalex.org/W2382532955","https://openalex.org/W2106962382","https://openalex.org/W4213342932","https://openalex.org/W2056379897","https://openalex.org/W2074316639","https://openalex.org/W2541927208","https://openalex.org/W4253114884","https://openalex.org/W2135860334"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,27,62],"method":[3,18,69,100],"for":[4,74],"conformational":[5],"search":[6],"of":[7,61,93,103,109],"complex":[8,110],"molecular":[9,28],"systems":[10,111],"such":[11],"as":[12],"macrocycles":[13],"and":[14,82,88],"protein":[15],"loops.":[16],"The":[17,68,91],"is":[19,53,70,78,101],"based":[20],"on":[21,39],"perturbing":[22],"an":[23],"existing":[24],"conformation":[25],"along":[26],"dynamics":[29],"trajectory":[30],"using":[31],"initial":[32],"atomic":[33],"velocities":[34],"with":[35,112],"kinetic":[36],"energy":[37,46,87,107],"concentrated":[38],"the":[40,58,99],"low-frequency":[41],"vibrational":[42],"modes,":[43],"followed":[44],"by":[45],"minimization.":[47],"A":[48],"novel":[49],"Chebyshev":[50],"polynomial":[51],"filter":[52],"used":[54],"to":[55,80],"heavily":[56],"dampen":[57],"high-frequency":[59],"components":[60],"randomly":[63],"generated":[64],"Maxwell-Boltzmann":[65],"velocity":[66],"vector.":[67],"very":[71],"efficient,":[72],"even":[73],"large":[75],"systems;":[76],"it":[77],"straightforward":[79],"implement":[81],"requires":[83],"only":[84],"standard":[85],"force-field":[86],"gradient":[89],"evaluations.":[90],"results":[92],"several":[94],"computational":[95],"experiments":[96],"suggest":[97],"that":[98],"capable":[102],"efficiently":[104],"sampling":[105],"low-strain":[106],"conformations":[108],"nontrivial":[113],"nonbonded":[114],"interaction":[115],"networks.":[116]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":29},{"year":2022,"cited_by_count":26},{"year":2021,"cited_by_count":32},{"year":2020,"cited_by_count":27},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":27},{"year":2017,"cited_by_count":24},{"year":2016,"cited_by_count":34},{"year":2015,"cited_by_count":16},{"year":2014,"cited_by_count":19},{"year":2013,"cited_by_count":17},{"year":2012,"cited_by_count":14}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
