{"id":"https://openalex.org/W3175731521","doi":"https://doi.org/10.1186/s13321-021-00528-w","title":"Optimized SQE atomic charges for peptides accessible via a web application","display_name":"Optimized SQE atomic charges for peptides accessible via a web application","publication_year":2021,"publication_date":"2021-06-30","ids":{"openalex":"https://openalex.org/W3175731521","doi":"https://doi.org/10.1186/s13321-021-00528-w","mag":"3175731521","pmid":"https://pubmed.ncbi.nlm.nih.gov/34193251"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-021-00528-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-021-00528-w","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-021-00528-w","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-021-00528-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058084999","display_name":"Ond\u0159ej Schindler","orcid":"https://orcid.org/0000-0002-9047-0334"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ond\u0159ej Schindler","raw_affiliation_strings":["CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040326443","display_name":"Tom\u00e1\u0161 Ra\u010dek","orcid":"https://orcid.org/0000-0002-0296-2452"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Tom\u00e1\u0161 Ra\u010dek","raw_affiliation_strings":["CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic","Faculty of Informatics, Masaryk University, Botanick\u00e1 68a, 602 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Faculty of Informatics, Masaryk University, Botanick\u00e1 68a, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031119477","display_name":"Aleksandra Mar\u0161avelski","orcid":"https://orcid.org/0000-0003-1139-7173"},"institutions":[{"id":"https://openalex.org/I181343428","display_name":"University of Zagreb","ror":"https://ror.org/00mv6sv71","country_code":"HR","type":"education","lineage":["https://openalex.org/I181343428"]}],"countries":["HR"],"is_corresponding":false,"raw_author_name":"Aleksandra Mar\u0161avelski","raw_affiliation_strings":["Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia","institution_ids":["https://openalex.org/I181343428"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061853775","display_name":"Jaroslav Ko\u010da","orcid":"https://orcid.org/0000-0002-2780-4901"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Jaroslav Ko\u010da","raw_affiliation_strings":["CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049457524","display_name":"Karel Berka","orcid":"https://orcid.org/0000-0001-9472-2589"},"institutions":[{"id":"https://openalex.org/I70703428","display_name":"Palack\u00fd University Olomouc","ror":"https://ror.org/04qxnmv42","country_code":"CZ","type":"education","lineage":["https://openalex.org/I70703428"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Karel Berka","raw_affiliation_strings":["Department of Physical Chemistry, Faculty of Science, Palack\u00fd University Olomouc, 17. listopadu 1192/12, 771 46, Olomouc, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physical Chemistry, Faculty of Science, Palack\u00fd University Olomouc, 17. listopadu 1192/12, 771 46, Olomouc, Czech Republic","institution_ids":["https://openalex.org/I70703428"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051424845","display_name":"Radka Svobodov\u00e1 Va\u0159ekov\u00e1","orcid":"https://orcid.org/0000-0002-3840-8760"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Radka Svobodov\u00e1","raw_affiliation_strings":["CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic. radka.svobodova@ceitec.muni.cz","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic. radka.svobodova@ceitec.muni.cz","National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic","CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic"],"raw_orcid":"https://orcid.org/0000-0002-3840-8760","affiliations":[{"raw_affiliation_string":"CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic. radka.svobodova@ceitec.muni.cz","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic. radka.svobodova@ceitec.muni.cz","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I21449261"]},{"raw_affiliation_string":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 602 00, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5051424845"],"corresponding_institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.2443,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.5264117,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"13","issue":"1","first_page":"45","last_page":"45"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.24230000376701355,"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":0.24230000376701355,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.1307000070810318,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.06870000064373016,"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/chemistry","display_name":"Chemistry","score":0.6505789160728455},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.5736772418022156},{"id":"https://openalex.org/keywords/charge","display_name":"Charge (physics)","score":0.5018565654754639},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4876948297023773},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45720818638801575},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.36907899379730225},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3442055583000183},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.34335052967071533},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3303040862083435}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6505789160728455},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.5736772418022156},{"id":"https://openalex.org/C188082385","wikidata":"https://www.wikidata.org/wiki/Q73792","display_name":"Charge (physics)","level":2,"score":0.5018565654754639},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4876948297023773},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45720818638801575},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.36907899379730225},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3442055583000183},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.34335052967071533},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3303040862083435},{"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-021-00528-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-021-00528-w","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-021-00528-w","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:34193251","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34193251","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:169dbc18d0964272ae4286310036a6f8","is_oa":true,"landing_page_url":"https://doaj.org/article/169dbc18d0964272ae4286310036a6f8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 13, Iss 1, Pp 1-11 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8243439","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8243439","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-021-00528-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-021-00528-w","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-021-00528-w","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1897300904","display_name":null,"funder_award_id":"INFRA LM2018140","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G5470076797","display_name":"e-Infrastructure CZ","funder_award_id":"LM2018140","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G5656519080","display_name":null,"funder_award_id":"e-INFRA LM2018140","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G954903593","display_name":"Czech National Infrastructure for Biological Data","funder_award_id":"LM2018131","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"}],"funders":[{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3175731521.pdf","grobid_xml":"https://content.openalex.org/works/W3175731521.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W370776269","https://openalex.org/W1650728208","https://openalex.org/W1732951662","https://openalex.org/W1968392598","https://openalex.org/W1976161355","https://openalex.org/W1983635605","https://openalex.org/W1984845825","https://openalex.org/W1993383767","https://openalex.org/W1997401744","https://openalex.org/W2002261888","https://openalex.org/W2009496113","https://openalex.org/W2042212021","https://openalex.org/W2049643865","https://openalex.org/W2051622977","https://openalex.org/W2072537419","https://openalex.org/W2074429159","https://openalex.org/W2085966856","https://openalex.org/W2088666833","https://openalex.org/W2097475255","https://openalex.org/W2107029002","https://openalex.org/W2170006871","https://openalex.org/W2183132306","https://openalex.org/W2316446502","https://openalex.org/W2539015190","https://openalex.org/W2588045278","https://openalex.org/W2601677732","https://openalex.org/W2773428214","https://openalex.org/W2788873578","https://openalex.org/W2792156980","https://openalex.org/W2899070097","https://openalex.org/W2981618201","https://openalex.org/W2982632536","https://openalex.org/W3025953134","https://openalex.org/W3033564049","https://openalex.org/W3080273308","https://openalex.org/W3110790550"],"related_works":["https://openalex.org/W1573015311","https://openalex.org/W2889938001","https://openalex.org/W4386509167","https://openalex.org/W3165034028","https://openalex.org/W1570419641","https://openalex.org/W4293771607","https://openalex.org/W2296499206","https://openalex.org/W132037564","https://openalex.org/W3210319767","https://openalex.org/W4246770172"],"abstract_inverted_index":{"BACKGROUND:":[0],"Partial":[1],"atomic":[2],"charges":[3],"find":[4],"many":[5],"applications":[6],"in":[7,240],"computational":[8],"chemistry,":[9],"chemoinformatics,":[10],"bioinformatics,":[11],"and":[12,31,59,74,84,98,130,154,165,171,216,261],"nanoscience.":[13],"Currently,":[14],"frequently":[15],"used":[16],"methods":[17,51,129,199,255],"for":[18,40,56,72,95,111,121,151,230,252],"charge":[19,66,127,253],"calculation":[20,67,128,254],"are":[21,37],"the":[22,79,112,122,134,158,174,192,205,208],"Electronegativity":[23],"Equalization":[24],"Method":[25],"(EEM),":[26],"Charge":[27,178],"Equilibration":[28,81],"method":[29,68,82,119],"(QEq),":[30],"Extended":[32],"QEq":[33,162],"(EQeq).":[34],"They":[35],"all":[36],"fast,":[38],"even":[39,48],"large":[41,265],"molecules,":[42],"but":[43],"require":[44],"empirical":[45,65,126],"parameters.":[46],"However,":[47],"these":[49,96],"advanced":[50],"have":[52],"limitations-e.g.,":[53],"their":[54,99,201],"application":[55,176,212],"peptides,":[57],"proteins,":[58],"other":[60,75],"macromolecules":[61],"is":[62,70,78,93,101,194],"problematic.":[63],"An":[64],"that":[69,195],"promising":[71],"peptides":[73],"macromolecular":[76],"systems":[77],"Split-charge":[80],"(SQE)":[83],"its":[85,262],"extension":[86,146],"SQE+q0.":[87,166],"Unfortunately,":[88],"only":[89],"one":[90],"parameter":[91,185],"set":[92],"available":[94,136],"methods,":[97],"implementation":[100],"not":[102],"easily":[103],"accessible.":[104],"RESULTS:":[105],"In":[106],"this":[107],"article,":[108],"we":[109,142,168],"present":[110],"first":[113],"time":[114],"an":[115,227],"optimized":[116],"guided":[117,137],"minimization":[118,138],"(optGM)":[120],"fast":[123],"parameterization":[124],"of":[125,191],"compare":[131,155],"it":[132,156,196],"with":[133,157,200,256],"currently":[135],"(GDMIN)":[139],"method.":[140],"Then,":[141],"introduce":[143],"a":[144,219,241],"further":[145],"to":[147,204,238,249],"SQE,":[148,164],"SQE+qp,":[149,225],"adapted":[150],"peptide":[152,231],"datasets,":[153],"common":[159],"approaches":[160],"EEM,":[161],"EQeq,":[163],"Finally,":[167],"integrate":[169],"SQE":[170,198,260],"SQE+qp":[172],"into":[173],"web":[175,211],"Atomic":[177],"Calculator":[179],"II":[180,210],"(ACC":[181],"II),":[182],"including":[183],"several":[184],"sets.":[186],"CONCLUSION:":[187],"The":[188],"main":[189],"contribution":[190],"article":[193],"makes":[197],"parameters":[202,237,258],"accessible":[203],"users":[206],"via":[207,218],"ACC":[209],"(":[213],"https://acc2.ncbr.muni.cz":[214],")":[215],"also":[217],"command-line":[220],"application.":[221],"Furthermore,":[222],"our":[223],"improvement,":[224],"provides":[226,235],"excellent":[228],"solution":[229],"datasets.":[232,266],"Additionally,":[233],"optGM":[234,246],"comparable":[236],"GDMIN":[239],"markedly":[242],"shorter":[243],"time.":[244],"Therefore,":[245],"allows":[247],"us":[248],"perform":[250],"parameterizations":[251],"more":[257],"(e.g.,":[259],"extensions)":[263],"using":[264]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
