{"id":"https://openalex.org/W4410317138","doi":"https://doi.org/10.1021/acs.jcim.5c00728","title":"PocketSCP: A Method for Spatiotemporal Topological Visualization and Analysis of Protein Pocket Dynamics","display_name":"PocketSCP: A Method for Spatiotemporal Topological Visualization and Analysis of Protein Pocket Dynamics","publication_year":2025,"publication_date":"2025-05-13","ids":{"openalex":"https://openalex.org/W4410317138","doi":"https://doi.org/10.1021/acs.jcim.5c00728","pmid":"https://pubmed.ncbi.nlm.nih.gov/40358406"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00728","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00728","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":null,"license_id":null,"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/A5101568547","display_name":"Dongliang Guo","orcid":"https://orcid.org/0000-0001-9935-7373"},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]},{"id":"https://openalex.org/I97750245","display_name":"Software (Spain)","ror":"https://ror.org/02ethns06","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210087817","https://openalex.org/I97750245"]}],"countries":["CN","ES"],"is_corresponding":true,"raw_author_name":"Dongliang Guo","raw_affiliation_strings":["School of Information Science and Engineering","The Key Laboratory for Software Engineering of Hebei Province","Yanshan University"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"The Key Laboratory for Software Engineering of Hebei Province","institution_ids":["https://openalex.org/I97750245"]},{"raw_affiliation_string":"Yanshan University","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103697054","display_name":"Hanqing Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hanqing Zhao","raw_affiliation_strings":["School of Information Science and Engineering","Yanshan University"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Yanshan University","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111188014","display_name":"J. S. Huang","orcid":"https://orcid.org/0009-0006-1243-2689"},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiabin Huang","raw_affiliation_strings":["School of Information Science and Engineering","Yanshan University"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Yanshan University","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106235913","display_name":"J. W. Zhao","orcid":"https://orcid.org/0009-0008-9337-2554"},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiawei Zhao","raw_affiliation_strings":["School of Information Science and Engineering","Yanshan University"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Yanshan University","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102816635","display_name":"Ximing Xu","orcid":"https://orcid.org/0000-0002-2125-7345"},"institutions":[{"id":"https://openalex.org/I4210145056","display_name":"Marine Biomedical Research Institute of Qingdao","ror":"https://ror.org/03pffnr86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210145056"]},{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ximing Xu","raw_affiliation_strings":["Marine Biomedical Research Institute of Qingdao","Ocean University of China","School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education"],"affiliations":[{"raw_affiliation_string":"Marine Biomedical Research Institute of Qingdao","institution_ids":["https://openalex.org/I4210145056"]},{"raw_affiliation_string":"Ocean University of China","institution_ids":["https://openalex.org/I59028903"]},{"raw_affiliation_string":"School of Medicine and Pharmacy, Key Laboratory of Marine Drugs, Chinese Ministry of Education","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054346946","display_name":"Yapeng Liu","orcid":"https://orcid.org/0009-0003-4680-619X"},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yapeng Liu","raw_affiliation_strings":["School of Information Science and Engineering","Yanshan University"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Yanshan University","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100451649","display_name":"Ying Yang","orcid":"https://orcid.org/0000-0002-8927-3878"},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Yang","raw_affiliation_strings":["Liren College","Yanshan University"],"affiliations":[{"raw_affiliation_string":"Liren College","institution_ids":[]},{"raw_affiliation_string":"Yanshan University","institution_ids":["https://openalex.org/I39333907"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5101568547"],"corresponding_institution_ids":["https://openalex.org/I39333907","https://openalex.org/I97750245"],"apc_list":null,"apc_paid":null,"fwci":1.6146,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.82746574,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"65","issue":"10","first_page":"5231","last_page":"5241"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9966999888420105,"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":0.9966999888420105,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9929999709129333,"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":0.9819999933242798,"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/visualization","display_name":"Visualization","score":0.7221772074699402},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5987892746925354},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5309270024299622},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.4647013545036316},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.38686954975128174},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.35144472122192383},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.30060723423957825},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.22672325372695923},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22654271125793457},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16681784391403198},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.0870174765586853}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7221772074699402},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5987892746925354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5309270024299622},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4647013545036316},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.38686954975128174},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35144472122192383},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30060723423957825},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.22672325372695923},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22654271125793457},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16681784391403198},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0870174765586853},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c00728","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00728","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40358406","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40358406","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":[],"awards":[{"id":"https://openalex.org/G1093572328","display_name":null,"funder_award_id":"22567637H","funder_id":"https://openalex.org/F4320324965","funder_display_name":"Hebei Provincial Department of Bureau of Science and Technology"},{"id":"https://openalex.org/G3234299039","display_name":null,"funder_award_id":"F2022203015","funder_id":"https://openalex.org/F4320322163","funder_display_name":"Natural Science Foundation of Hebei Province"},{"id":"https://openalex.org/G5447342375","display_name":null,"funder_award_id":"61802334","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322163","display_name":"Natural Science Foundation of Hebei Province","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324965","display_name":"Hebei Provincial Department of Bureau of Science and Technology","ror":"https://ror.org/05k812a28"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1517566065","https://openalex.org/W2004863845","https://openalex.org/W2009874233","https://openalex.org/W2019951137","https://openalex.org/W2027687260","https://openalex.org/W2031194866","https://openalex.org/W2041205020","https://openalex.org/W2051182208","https://openalex.org/W2058463742","https://openalex.org/W2062884696","https://openalex.org/W2069207477","https://openalex.org/W2071980307","https://openalex.org/W2088204921","https://openalex.org/W2091563009","https://openalex.org/W2105902442","https://openalex.org/W2107278499","https://openalex.org/W2112794559","https://openalex.org/W2116703791","https://openalex.org/W2125385744","https://openalex.org/W2128402268","https://openalex.org/W2131777290","https://openalex.org/W2134468204","https://openalex.org/W2140544024","https://openalex.org/W2158076215","https://openalex.org/W2160715766","https://openalex.org/W2163577738","https://openalex.org/W2163816950","https://openalex.org/W2164088236","https://openalex.org/W2166225722","https://openalex.org/W2267582375","https://openalex.org/W2334874683","https://openalex.org/W2403767926","https://openalex.org/W2417567863","https://openalex.org/W2467187082","https://openalex.org/W2513636825","https://openalex.org/W2605604484","https://openalex.org/W2742394249","https://openalex.org/W2802974816","https://openalex.org/W2888840714","https://openalex.org/W2954835418","https://openalex.org/W3003883816","https://openalex.org/W3038901077","https://openalex.org/W4306652138","https://openalex.org/W4398222244"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2081517010","https://openalex.org/W2121496884","https://openalex.org/W2387910809","https://openalex.org/W2294221496"],"abstract_inverted_index":{"The":[0],"identification":[1],"and":[2,13,40,62,88],"analysis":[3,41],"of":[4,16,27,42,51,65,83,107,113],"pockets":[5,122],"are":[6],"crucial":[7],"for":[8,37],"understanding":[9],"the":[10,24,28,38,49,60,103,111],"functional":[11],"mechanisms":[12],"therapeutic":[14],"potential":[15,118],"proteins.":[17],"However,":[18],"it":[19],"is":[20,56,76,100,123],"challenging":[21],"to":[22,58,78,91],"track":[23],"dynamic":[25],"characteristics":[26],"pockets.":[29,66,84],"In":[30],"this":[31],"paper,":[32],"we":[33],"present":[34],"a":[35,72],"method":[36,115],"visualization":[39],"protein":[43,108,121],"pocket":[44],"dynamics":[45],"called":[46],"PocketSCP.":[47],"Initially,":[48],"representation":[50],"lining":[52],"amino":[53],"acid":[54],"atoms":[55],"proposed":[57],"characterize":[59],"spatiotemporal":[61],"topological":[63],"properties":[64,106],"Subsequently,":[67],"3D":[68,80,90],"mapping":[69,94],"based":[70,95],"on":[71,96],"reference":[73],"molecular":[74],"conformation":[75],"designed":[77],"generate":[79],"distribution":[81],"maps":[82],"To":[85],"facilitate":[86],"observation":[87],"analysis,":[89],"2D":[92],"plane":[93],"equidistant":[97],"azimuthal":[98],"projection":[99],"designed,":[101],"leveraging":[102],"near-spherical":[104],"shape":[105],"molecules.":[109],"Finally,":[110],"efficacy":[112],"our":[114],"in":[116],"identifying":[117],"patterns":[119],"within":[120],"demonstrated":[124],"through":[125],"experimental":[126],"validation.":[127]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
