{"id":"https://openalex.org/W2601198875","doi":"https://doi.org/10.1021/acs.jcim.7b00096","title":"PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories","display_name":"PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories","publication_year":2017,"publication_date":"2017-03-27","ids":{"openalex":"https://openalex.org/W2601198875","doi":"https://doi.org/10.1021/acs.jcim.7b00096","mag":"2601198875","pmid":"https://pubmed.ncbi.nlm.nih.gov/28345910"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.7b00096","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00096","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/A5010526590","display_name":"James Graham","orcid":"https://orcid.org/0000-0001-5217-3104"},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"James A. Graham","raw_affiliation_strings":["School of Chemistry, University of Southampton, Hampshire, SO17 1BJ, United Kingdom","University of Southampton, Chemistry Essex, Jonathan; University of Southampton, School of Chemistry Khalid, Syma; University of Southampton, Chemistry"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chemistry, University of Southampton, Hampshire, SO17 1BJ, United Kingdom","institution_ids":["https://openalex.org/I43439940"]},{"raw_affiliation_string":"University of Southampton, Chemistry Essex, Jonathan; University of Southampton, School of Chemistry Khalid, Syma; University of Southampton, Chemistry","institution_ids":["https://openalex.org/I43439940"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067820273","display_name":"Jonathan W. Essex","orcid":"https://orcid.org/0000-0003-2639-2746"},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jonathan W. Essex","raw_affiliation_strings":["School of Chemistry, University of Southampton, Hampshire, SO17 1BJ, United Kingdom","University of Southampton, Chemistry Essex, Jonathan; University of Southampton, School of Chemistry Khalid, Syma; University of Southampton, Chemistry"],"raw_orcid":"https://orcid.org/0000-0003-2639-2746","affiliations":[{"raw_affiliation_string":"School of Chemistry, University of Southampton, Hampshire, SO17 1BJ, United Kingdom","institution_ids":["https://openalex.org/I43439940"]},{"raw_affiliation_string":"University of Southampton, Chemistry Essex, Jonathan; University of Southampton, School of Chemistry Khalid, Syma; University of Southampton, Chemistry","institution_ids":["https://openalex.org/I43439940"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079670006","display_name":"Syma Khalid","orcid":"https://orcid.org/0000-0002-3694-5044"},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"education","lineage":["https://openalex.org/I43439940"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Syma Khalid","raw_affiliation_strings":["School of Chemistry, University of Southampton, Hampshire, SO17 1BJ, United Kingdom","University of Southampton, Chemistry Essex, Jonathan; University of Southampton, School of Chemistry Khalid, Syma; University of Southampton, Chemistry"],"raw_orcid":"https://orcid.org/0000-0002-3694-5044","affiliations":[{"raw_affiliation_string":"School of Chemistry, University of Southampton, Hampshire, SO17 1BJ, United Kingdom","institution_ids":["https://openalex.org/I43439940"]},{"raw_affiliation_string":"University of Southampton, Chemistry Essex, Jonathan; University of Southampton, School of Chemistry Khalid, Syma; University of Southampton, Chemistry","institution_ids":["https://openalex.org/I43439940"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5079670006"],"corresponding_institution_ids":["https://openalex.org/I43439940"],"apc_list":null,"apc_paid":null,"fwci":2.7758,"has_fulltext":false,"cited_by_count":107,"citation_normalized_percentile":{"value":0.91359444,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"57","issue":"4","first_page":"650","last_page":"656"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11471","display_name":"Block Copolymer Self-Assembly","score":0.9993000030517578,"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"}},"topics":[{"id":"https://openalex.org/T11471","display_name":"Block Copolymer Self-Assembly","score":0.9993000030517578,"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"}},{"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/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.8276021480560303},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7136574983596802},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5854368209838867},{"id":"https://openalex.org/keywords/parametrization","display_name":"Parametrization (atmospheric modeling)","score":0.5537704229354858},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.5348834991455078},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4734492003917694},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.47048261761665344},{"id":"https://openalex.org/keywords/bespoke","display_name":"Bespoke","score":0.44324713945388794},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.42929571866989136},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.4244828224182129},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35957956314086914},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.23354414105415344},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.20614689588546753},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1937093436717987},{"id":"https://openalex.org/keywords/mechanical-engineering","display_name":"Mechanical engineering","score":0.126024067401886},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09400364756584167}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.8276021480560303},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7136574983596802},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5854368209838867},{"id":"https://openalex.org/C202887219","wikidata":"https://www.wikidata.org/wiki/Q3895221","display_name":"Parametrization (atmospheric modeling)","level":3,"score":0.5537704229354858},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.5348834991455078},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4734492003917694},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.47048261761665344},{"id":"https://openalex.org/C44210515","wikidata":"https://www.wikidata.org/wiki/Q16968978","display_name":"Bespoke","level":2,"score":0.44324713945388794},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.42929571866989136},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4244828224182129},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35957956314086914},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23354414105415344},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.20614689588546753},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1937093436717987},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.126024067401886},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09400364756584167},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"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/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C74902906","wikidata":"https://www.wikidata.org/wiki/Q1190858","display_name":"Radiative transfer","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","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":"D008968","descriptor_name":"Molecular Conformation","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.7b00096","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00096","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:28345910","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28345910","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},{"id":"pmh:oai:eprints.soton.ac.uk:408522","is_oa":false,"landing_page_url":"http://doi.org/10.1021/acs.jcim.7b00096>).","pdf_url":null,"source":{"id":"https://openalex.org/S4306401019","display_name":"ePrints Soton (University of Southampton)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1407783600","display_name":"A Doctoral Training Centre in Complex Systems Simulations","funder_award_id":"EP/G03690X/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G1592560434","display_name":null,"funder_award_id":"EP/G042853/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G1717999737","display_name":null,"funder_award_id":"BB/L018756/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2513858435","display_name":null,"funder_award_id":"BB/H000658/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G3583580618","display_name":null,"funder_award_id":"BB/K016601/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G381020761","display_name":"OMSys: Towards a systems model of a bacterial outer membrane","funder_award_id":"BB/H000658/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4706702539","display_name":"CCP-BioSim: Biomolecular Simulation at the Life Sciences Interface","funder_award_id":"EP/M022609/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5758995618","display_name":null,"funder_award_id":"EP/M022609/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6148688325","display_name":null,"funder_award_id":"EP/M027546/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6504168431","display_name":"Adaptive Multi-Resolution Massively-Multicore Hybrid Dynamics","funder_award_id":"EP/I030395/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7814653466","display_name":null,"funder_award_id":"EP/I030395/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G783393384","display_name":null,"funder_award_id":"EP/J010588/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8294306494","display_name":null,"funder_award_id":"EP/G007705/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8947107902","display_name":null,"funder_award_id":"EP/L000253/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1963731008","https://openalex.org/W2016094489","https://openalex.org/W2018659143","https://openalex.org/W2019465613","https://openalex.org/W2035500672","https://openalex.org/W2038302435","https://openalex.org/W2047796232","https://openalex.org/W2058366932","https://openalex.org/W2060487344","https://openalex.org/W2061308254","https://openalex.org/W2081724315","https://openalex.org/W2086946786","https://openalex.org/W2098943363","https://openalex.org/W2127522551","https://openalex.org/W2147988069","https://openalex.org/W2164730735","https://openalex.org/W2171727742","https://openalex.org/W2430893910","https://openalex.org/W2465557450","https://openalex.org/W2540602443","https://openalex.org/W3155828254"],"related_works":["https://openalex.org/W2181465263","https://openalex.org/W3093969907","https://openalex.org/W3202725889","https://openalex.org/W2232750048","https://openalex.org/W2212726445","https://openalex.org/W4244794230","https://openalex.org/W4389712339","https://openalex.org/W2806540758","https://openalex.org/W2494533090","https://openalex.org/W3082526343"],"abstract_inverted_index":{"Development":[0],"of":[1,27,30,35,42,54,63,71,87,89,95,116],"coarse-grained":[2],"(CG)":[3],"molecular":[4,48,111],"dynamics":[5,49,112],"models":[6,32],"is":[7,124,133],"often":[8],"a":[9],"laborious":[10],"process":[11],"which":[12],"commonly":[13],"relies":[14],"upon":[15],"approximations":[16],"to":[17,68],"similar":[18],"models,":[19],"rather":[20],"than":[21],"systematic":[22],"parametrization.":[23],"PyCGTOOL":[24,90,104],"automates":[25],"much":[26],"the":[28,61,64,69,82,92,109,136,140],"construction":[29],"CG":[31,65],"via":[33],"calculation":[34],"both":[36],"equilibrium":[37],"values":[38],"and":[39,99],"force":[40],"constants":[41],"internal":[43],"coordinates":[44],"directly":[45],"from":[46,57,75,135],"atomistic":[47,58],"simulation":[50],"trajectories.":[51],"The":[52,85,131],"derivation":[53],"bespoke":[55],"parameters":[56,73],"simulations":[59],"improves":[60],"quality":[62],"model":[66],"compared":[67],"use":[70,115],"generic":[72],"derived":[74],"other":[76,129],"molecules,":[77],"while":[78],"automation":[79],"greatly":[80],"reduces":[81],"time":[83],"required.":[84],"ease":[86],"configuration":[88],"enables":[91],"rapid":[93],"investigation":[94],"multiple":[96],"atom-to-bead":[97],"mappings":[98],"topologies.":[100],"Although":[101],"we":[102],"present":[103],"used":[105],"in":[106,125],"combination":[107],"with":[108,128],"GROMACS":[110],"engine":[113],"its":[114],"standard":[117],"trajectory":[118],"input":[119],"libraries":[120],"means":[121],"that":[122],"it":[123],"principle":[126],"compatible":[127],"software.":[130],"software":[132],"available":[134],"URL":[137],"https://github.com/jag1g13/pycgtool":[138],"as":[139],"following":[141],"doi:":[142],"10.5281/zenodo.259330":[143],".":[144]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":3}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
