{"id":"https://openalex.org/W4404115367","doi":"https://doi.org/10.1021/acs.jcim.4c01710","title":"Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations","display_name":"Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations","publication_year":2024,"publication_date":"2024-11-06","ids":{"openalex":"https://openalex.org/W4404115367","doi":"https://doi.org/10.1021/acs.jcim.4c01710","pmid":"https://pubmed.ncbi.nlm.nih.gov/39501568"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01710","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01710","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":true,"oa_status":"green","oa_url":"https://escholarship.org/content/qt7723n8bn/qt7723n8bn.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082893610","display_name":"Benjamin Ries","orcid":"https://orcid.org/0000-0002-0945-8304"},"institutions":[{"id":"https://openalex.org/I1330995197","display_name":"Boehringer Ingelheim (Germany)","ror":"https://ror.org/00q32j219","country_code":"DE","type":"company","lineage":["https://openalex.org/I1330995197"]},{"id":"https://openalex.org/I40695006","display_name":"Open Geospatial Consortium","ror":"https://ror.org/00fsdxs93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40695006"]},{"id":"https://openalex.org/I4400573198","display_name":"Open Molecular Software Foundation","ror":"https://ror.org/02en65a92","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4400573198"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Benjamin Ries","raw_affiliation_strings":["Boehringer Ingelheim Pharma GmbH & Co KG, Medicinal Chemistry, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany","Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States"],"affiliations":[{"raw_affiliation_string":"Boehringer Ingelheim Pharma GmbH & Co KG, Medicinal Chemistry, Birkendorfer Str. 65, 88397 Biberach an der Riss, Germany","institution_ids":["https://openalex.org/I1330995197"]},{"raw_affiliation_string":"Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States","institution_ids":["https://openalex.org/I40695006","https://openalex.org/I4400573198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067172880","display_name":"Richard Gowers","orcid":"https://orcid.org/0000-0002-3241-1846"},"institutions":[{"id":"https://openalex.org/I40695006","display_name":"Open Geospatial Consortium","ror":"https://ror.org/00fsdxs93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40695006"]},{"id":"https://openalex.org/I4400573198","display_name":"Open Molecular Software Foundation","ror":"https://ror.org/02en65a92","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4400573198"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard J. Gowers","raw_affiliation_strings":["Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States"],"affiliations":[{"raw_affiliation_string":"Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States","institution_ids":["https://openalex.org/I40695006","https://openalex.org/I4400573198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037903278","display_name":"Hannah M. Baumann","orcid":"https://orcid.org/0000-0002-1736-7744"},"institutions":[{"id":"https://openalex.org/I40695006","display_name":"Open Geospatial Consortium","ror":"https://ror.org/00fsdxs93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40695006"]},{"id":"https://openalex.org/I4400573198","display_name":"Open Molecular Software Foundation","ror":"https://ror.org/02en65a92","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4400573198"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hannah M. Baumann","raw_affiliation_strings":["Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States"],"affiliations":[{"raw_affiliation_string":"Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States","institution_ids":["https://openalex.org/I40695006","https://openalex.org/I4400573198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052616501","display_name":"David A. Swenson","orcid":"https://orcid.org/0000-0001-9922-7923"},"institutions":[{"id":"https://openalex.org/I40695006","display_name":"Open Geospatial Consortium","ror":"https://ror.org/00fsdxs93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40695006"]},{"id":"https://openalex.org/I4400573198","display_name":"Open Molecular Software Foundation","ror":"https://ror.org/02en65a92","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4400573198"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David W. H. Swenson","raw_affiliation_strings":["Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States"],"affiliations":[{"raw_affiliation_string":"Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States","institution_ids":["https://openalex.org/I40695006","https://openalex.org/I4400573198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041383248","display_name":"Michael M. Henry","orcid":"https://orcid.org/0000-0002-3870-9993"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I40695006","display_name":"Open Geospatial Consortium","ror":"https://ror.org/00fsdxs93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40695006"]},{"id":"https://openalex.org/I4400573198","display_name":"Open Molecular Software Foundation","ror":"https://ror.org/02en65a92","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4400573198"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael M. Henry","raw_affiliation_strings":["Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States","Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States"],"affiliations":[{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States","institution_ids":["https://openalex.org/I40695006","https://openalex.org/I4400573198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063413637","display_name":"James R. B. Eastwood","orcid":"https://orcid.org/0000-0003-3895-5227"},"institutions":[{"id":"https://openalex.org/I40695006","display_name":"Open Geospatial Consortium","ror":"https://ror.org/00fsdxs93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40695006"]},{"id":"https://openalex.org/I4400573198","display_name":"Open Molecular Software Foundation","ror":"https://ror.org/02en65a92","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4400573198"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James R. B. Eastwood","raw_affiliation_strings":["Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States"],"affiliations":[{"raw_affiliation_string":"Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States","institution_ids":["https://openalex.org/I40695006","https://openalex.org/I4400573198"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019650412","display_name":"Irfan Alibay","orcid":"https://orcid.org/0000-0001-5787-9130"},"institutions":[{"id":"https://openalex.org/I40695006","display_name":"Open Geospatial Consortium","ror":"https://ror.org/00fsdxs93","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40695006"]},{"id":"https://openalex.org/I4400573198","display_name":"Open Molecular Software Foundation","ror":"https://ror.org/02en65a92","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4400573198"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Irfan Alibay","raw_affiliation_strings":["Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States"],"affiliations":[{"raw_affiliation_string":"Open Free Energy, Open Molecular Software Foundation, Davis, California 95616, United States","institution_ids":["https://openalex.org/I40695006","https://openalex.org/I4400573198"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007496868","display_name":"David L. Mobley","orcid":"https://orcid.org/0000-0002-1083-5533"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Mobley","raw_affiliation_strings":["Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine, California 92617, United States"],"affiliations":[{"raw_affiliation_string":"Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine, California 92617, United States","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5082893610"],"corresponding_institution_ids":["https://openalex.org/I1330995197","https://openalex.org/I40695006","https://openalex.org/I4400573198"],"apc_list":null,"apc_paid":null,"fwci":0.5517,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.6589868,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"64","issue":"22","first_page":"8396","last_page":"8403"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9905999898910522,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.978600025177002,"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/graph-theory","display_name":"Graph theory","score":0.5940982699394226},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5253509879112244},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5090686678886414},{"id":"https://openalex.org/keywords/plan","display_name":"Plan (archaeology)","score":0.45460575819015503},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.44293415546417236},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3728994131088257},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.30306729674339294},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.21644729375839233},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.1943836510181427},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10437420010566711}],"concepts":[{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.5940982699394226},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5253509879112244},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5090686678886414},{"id":"https://openalex.org/C2776505523","wikidata":"https://www.wikidata.org/wiki/Q4785468","display_name":"Plan (archaeology)","level":2,"score":0.45460575819015503},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.44293415546417236},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3728994131088257},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.30306729674339294},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.21644729375839233},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1943836510181427},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10437420010566711},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.4c01710","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01710","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:39501568","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39501568","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:escholarship.org:ark:/13030/qt7723n8bn","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7723n8bn","pdf_url":"https://escholarship.org/content/qt7723n8bn/qt7723n8bn.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of chemical information and computer sciences, vol 64, iss 22","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11812579","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11812579","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11812579/pdf/nihms-2046857.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:escholarship.org:ark:/13030/qt7723n8bn","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7723n8bn","pdf_url":"https://escholarship.org/content/qt7723n8bn/qt7723n8bn.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of chemical information and computer sciences, vol 64, iss 22","raw_type":"article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8100000023841858,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2152107955","display_name":null,"funder_award_id":"GM148236","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2571516994","display_name":null,"funder_award_id":"R35GM14823","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7481435163","display_name":null,"funder_award_id":"R35GM148236","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404115367.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1625910593","https://openalex.org/W1965680834","https://openalex.org/W1970973025","https://openalex.org/W2011301426","https://openalex.org/W2023222460","https://openalex.org/W2044834685","https://openalex.org/W2061939373","https://openalex.org/W2072604508","https://openalex.org/W2073714240","https://openalex.org/W2093755925","https://openalex.org/W2103034037","https://openalex.org/W2104630281","https://openalex.org/W2132022337","https://openalex.org/W2146292423","https://openalex.org/W2151020862","https://openalex.org/W2154670681","https://openalex.org/W2159675211","https://openalex.org/W2180566385","https://openalex.org/W2323942455","https://openalex.org/W2535858809","https://openalex.org/W2552522590","https://openalex.org/W2768019189","https://openalex.org/W2772606519","https://openalex.org/W2941138866","https://openalex.org/W2967253501","https://openalex.org/W2985021042","https://openalex.org/W2990010612","https://openalex.org/W3003498601","https://openalex.org/W3034934060","https://openalex.org/W3035285619","https://openalex.org/W3036993656","https://openalex.org/W3042009478","https://openalex.org/W3118488899","https://openalex.org/W3183881215","https://openalex.org/W3201039087","https://openalex.org/W4286855287","https://openalex.org/W4293113010","https://openalex.org/W4294679529","https://openalex.org/W4298125158","https://openalex.org/W4313128019","https://openalex.org/W4315433138","https://openalex.org/W4323308282","https://openalex.org/W4365810972","https://openalex.org/W4376129086","https://openalex.org/W4389396422","https://openalex.org/W4399356565","https://openalex.org/W6969257490"],"related_works":["https://openalex.org/W2072180474","https://openalex.org/W1960052459","https://openalex.org/W2375707231","https://openalex.org/W2524555411","https://openalex.org/W3209137209","https://openalex.org/W2532801570","https://openalex.org/W4385627933","https://openalex.org/W2480127678","https://openalex.org/W2806270048","https://openalex.org/W4310605282"],"abstract_inverted_index":{"Alchemical":[0],"free":[1,39,59],"energy":[2,40,60],"campaigns":[3,61],"can":[4,155],"be":[5,156],"planned":[6],"using":[7,62,121],"graph":[8,64,166],"theory":[9,167],"by":[10,21,53],"building":[11],"networks":[12,162],"that":[13,18],"contain":[14],"nodes":[15],"representing":[16],"molecules":[17,84],"are":[19],"connected":[20],"possible":[22],"transformations":[23],"as":[24],"edges.":[25],"We":[26],"introduce":[27],"Konnektor,":[28],"an":[29],"open-source":[30],"Python":[31],"package,":[32,145],"for":[33,71,89,106],"systematically":[34],"planning,":[35],"modifying,":[36],"and":[37,81,129,158],"analyzing":[38],"calculation":[41],"networks.":[42],"Konnektor":[43,126,154,169],"is":[44,118,170],"designed":[45],"to":[46,56,98],"aid":[47],"in":[48],"the":[49,100,112,133,141,144,146,160,178],"drug":[50],"discovery":[51],"process":[52],"enabling":[54],"users":[55],"easily":[57],"setup":[58],"complex":[63,104],"manipulation":[65],"methods.":[66],"The":[67],"package":[68],"contains":[69,127],"functions":[70],"network":[72,95,107,114,136],"operations":[73],"including":[74],"concatenation":[75],"of":[76,79,83,102,111,135,143],"networks,":[77],"deletion":[78],"transformations,":[80],"clustering":[82],"along":[85],"with":[86,93],"a":[87,165],"framework":[88],"combining":[90],"these":[91],"tools":[92],"existing":[94],"generation":[96],"algorithms":[97],"enable":[99],"development":[101],"more":[103],"methods":[105],"generation.":[108],"A":[109],"comparison":[110],"various":[113],"layout":[115],"features":[116,137],"offered":[117],"carried":[119],"out":[120],"toy":[122],"data":[123],"sets.":[124],"Additionally,":[125],"visualization":[128],"analysis":[130],"tools,":[131],"making":[132],"investigation":[134],"much":[138],"simpler.":[139],"Besides":[140],"content":[142],"paper":[147],"also":[148],"offers":[149],"application":[150],"examples,":[151],"demonstrating":[152],"how":[153,159],"used":[157],"different":[161],"perform":[163],"from":[164],"perspective.":[168],"freely":[171],"available":[172],"via":[173],"GitHub":[174],"at":[175],"https://github.com/OpenFreeEnergy/konnektor":[176],"under":[177],"permissive":[179],"MIT":[180],"License.":[181]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
