{"id":"https://openalex.org/W4409834754","doi":"https://doi.org/10.1021/acs.jcim.5c00041","title":"PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges","display_name":"PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges","publication_year":2025,"publication_date":"2025-04-26","ids":{"openalex":"https://openalex.org/W4409834754","doi":"https://doi.org/10.1021/acs.jcim.5c00041","pmid":"https://pubmed.ncbi.nlm.nih.gov/40285710"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00041","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00041","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/A5115805180","display_name":"Marco Lapsien","orcid":null},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marco Lapsien","raw_affiliation_strings":["Heinrich Heine University D\u00fcsseldorf","Institute for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science Center (BioSC)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Heinrich Heine University D\u00fcsseldorf","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science Center (BioSC)","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027647645","display_name":"Michele Bonus","orcid":"https://orcid.org/0000-0003-4411-7342"},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michele Bonus","raw_affiliation_strings":["Heinrich Heine University D\u00fcsseldorf","Institute for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science Center (BioSC)"],"raw_orcid":"https://orcid.org/0000-0003-4411-7342","affiliations":[{"raw_affiliation_string":"Heinrich Heine University D\u00fcsseldorf","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science Center (BioSC)","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lianne Gahan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210143403","display_name":"Norwegian Institute of Bioeconomy Research","ror":"https://ror.org/04aah1z61","country_code":"NO","type":"funder","lineage":["https://openalex.org/I4210143403"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE","NO"],"is_corresponding":false,"raw_author_name":"Lianne Gahan","raw_affiliation_strings":["Heinrich Heine University D\u00fcsseldorf","Institute for Computational Cell Biology & Bioeconomy Science Center (BioSC)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Heinrich Heine University D\u00fcsseldorf","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute for Computational Cell Biology & Bioeconomy Science Center (BioSC)","institution_ids":["https://openalex.org/I4210143403"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050021188","display_name":"Ad\u00e9la\u00efde Raguin","orcid":"https://orcid.org/0000-0003-0057-7021"},"institutions":[{"id":"https://openalex.org/I4210143403","display_name":"Norwegian Institute of Bioeconomy Research","ror":"https://ror.org/04aah1z61","country_code":"NO","type":"funder","lineage":["https://openalex.org/I4210143403"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE","NO"],"is_corresponding":false,"raw_author_name":"Ad\u00e9la\u00efde Raguin","raw_affiliation_strings":["Heinrich Heine University D\u00fcsseldorf","Institute for Computational Cell Biology & Bioeconomy Science Center (BioSC)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Heinrich Heine University D\u00fcsseldorf","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute for Computational Cell Biology & Bioeconomy Science Center (BioSC)","institution_ids":["https://openalex.org/I4210143403"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063949219","display_name":"Holger Gohlke","orcid":"https://orcid.org/0000-0001-8613-1447"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Holger Gohlke","raw_affiliation_strings":["Forschungszentrum J\u00fclich","Heinrich Heine University D\u00fcsseldorf","Institute for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science Center (BioSC)","Institute of Bio- and Geosciences (IBG-4: Bioinformatics)"],"raw_orcid":"https://orcid.org/0000-0001-8613-1447","affiliations":[{"raw_affiliation_string":"Forschungszentrum J\u00fclich","institution_ids":["https://openalex.org/I171892758"]},{"raw_affiliation_string":"Heinrich Heine University D\u00fcsseldorf","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science Center (BioSC)","institution_ids":[]},{"raw_affiliation_string":"Institute of Bio- and Geosciences (IBG-4: Bioinformatics)","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5063949219"],"corresponding_institution_ids":["https://openalex.org/I171892758","https://openalex.org/I44260953"],"apc_list":null,"apc_paid":null,"fwci":3.1878,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.91419411,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"65","issue":"9","first_page":"4251","last_page":"4256"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9973000288009644,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9926999807357788,"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/computer-science","display_name":"Computer science","score":0.4576209783554077}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4576209783554077}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","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":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.5c00041","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00041","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:40285710","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40285710","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/G1659070430","display_name":null,"funder_award_id":"EXC 2048/1 390686111","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2265337514","display_name":null,"funder_award_id":"313/323-400-002 13","funder_id":"https://openalex.org/F4320325901","funder_display_name":"Ministerium f\u00fcr Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320325901","display_name":"Ministerium f\u00fcr Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1976161355","https://openalex.org/W2029667189","https://openalex.org/W2041902442","https://openalex.org/W2068629260","https://openalex.org/W2070753604","https://openalex.org/W2075093176","https://openalex.org/W2076497939","https://openalex.org/W2131288855","https://openalex.org/W2147993766","https://openalex.org/W2167029191","https://openalex.org/W2433523887","https://openalex.org/W2613386458","https://openalex.org/W2790441008","https://openalex.org/W2969567271","https://openalex.org/W2989052455","https://openalex.org/W4242512501","https://openalex.org/W4280532514","https://openalex.org/W4295880919","https://openalex.org/W4317989686","https://openalex.org/W4386501989","https://openalex.org/W4387440676","https://openalex.org/W4392093336","https://openalex.org/W4401544502"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"We":[0],"introduce":[1],"PyPE_RESP,":[2],"a":[3,50,61],"tool":[4],"to":[5,95],"facilitate":[6],"and":[7,30,44,83,91,110],"standardize":[8],"partial":[9,78],"atomic":[10,79],"charge":[11,54],"derivation":[12,76],"using":[13],"the":[14,23,31,75,101],"Restrained":[15],"Electrostatic":[16],"Potential":[17],"(RESP)":[18],"approach.":[19],"PyPE_RESP":[20,37,65,104],"builds":[21],"upon":[22],"open-source":[24],"Python":[25],"package":[26],"RDKit":[27],"for":[28,34,81],"chemoinformatics":[29],"AMBER":[32],"suite":[33],"molecular":[35],"simulations.":[36],"provides":[38],"an":[39,97],"easy":[40],"setup":[41],"of":[42,53,77,100],"multiconformer":[43],"multimolecule":[45],"RESP":[46],"fitting":[47],"while":[48],"allowing":[49],"comprehensive":[51],"definition":[52],"constraint":[55,89],"groups":[56],"through":[57],"multiple":[58],"methods.":[59],"As":[60],"command":[62],"line":[63],"tool,":[64],"can":[66],"be":[67,106],"integrated":[68],"into":[69],"batch":[70],"processes.":[71],"The":[72],"software":[73],"enables":[74],"charges":[80,94],"additive":[82],"polarizable":[84],"force":[85],"fields.":[86],"It":[87],"outputs":[88],"group":[90,93],"nonconstraint":[92],"give":[96],"immediate":[98],"overview":[99],"fit":[102],"result.":[103],"will":[105],"distributed":[107],"with":[108,112],"AmberTools":[109],"compatible":[111],"most":[113],"computing":[114],"platforms.":[115]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-20T08:49:12.498775","created_date":"2025-10-10T00:00:00"}
