{"id":"https://openalex.org/W2784238781","doi":"https://doi.org/10.1007/s10822-018-0097-y","title":"Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors","display_name":"Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors","publication_year":2018,"publication_date":"2018-01-14","ids":{"openalex":"https://openalex.org/W2784238781","doi":"https://doi.org/10.1007/s10822-018-0097-y","mag":"2784238781","pmid":"https://pubmed.ncbi.nlm.nih.gov/29335871"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-018-0097-y","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-018-0097-y","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","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/A5063702078","display_name":"Zolt\u00e1n Orgov\u00e1n","orcid":"https://orcid.org/0000-0002-8002-3047"},"institutions":[{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"Zolt\u00e1n Orgov\u00e1n","raw_affiliation_strings":["Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I80251312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078470424","display_name":"Gy\u00f6rgy G. Ferenczy","orcid":"https://orcid.org/0000-0002-5771-4616"},"institutions":[{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Gy\u00f6rgy G. Ferenczy","raw_affiliation_strings":["Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I80251312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047628202","display_name":"Thomas Steinbrecher","orcid":"https://orcid.org/0000-0003-4103-2968"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thomas Steinbrecher","raw_affiliation_strings":["Schr\u00f6dinger GmbH, Dynamostr. 13, 68165, Mannheim, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger GmbH, Dynamostr. 13, 68165, Mannheim, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091231195","display_name":"Bence Szil\u00e1gyi","orcid":"https://orcid.org/0000-0002-3498-1041"},"institutions":[{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Bence Szil\u00e1gyi","raw_affiliation_strings":["Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I80251312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026174702","display_name":"D\u00e1vid Bajusz","orcid":"https://orcid.org/0000-0003-4277-9481"},"institutions":[{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"D\u00e1vid Bajusz","raw_affiliation_strings":["Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I80251312"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022888378","display_name":"Gy\u00f6rgy M. Keser\u0171","orcid":"https://orcid.org/0000-0003-1039-7809"},"institutions":[{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Gy\u00f6rgy M. Keser\u0171","raw_affiliation_strings":["Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary. gy.keseru@ttk.mta.hu","Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary"],"raw_orcid":"https://orcid.org/0000-0003-1039-7809","affiliations":[{"raw_affiliation_string":"Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary. gy.keseru@ttk.mta.hu","institution_ids":["https://openalex.org/I80251312"]},{"raw_affiliation_string":"Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tud\u00f3sok krt. 2, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I80251312"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5063702078"],"corresponding_institution_ids":["https://openalex.org/I80251312"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":1.0821,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.7430622,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"32","issue":"2","first_page":"331","last_page":"345"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12770","display_name":"Amino Acid Enzymes and Metabolism","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1303","display_name":"Biochemistry"},"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/T12770","display_name":"Amino Acid Enzymes and Metabolism","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1303","display_name":"Biochemistry"},"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9977999925613403,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9973000288009644,"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/indazole","display_name":"Indazole","score":0.8520257472991943},{"id":"https://openalex.org/keywords/isoxazole","display_name":"Isoxazole","score":0.8380545377731323},{"id":"https://openalex.org/keywords/tautomer","display_name":"Tautomer","score":0.8280671238899231},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.819334864616394},{"id":"https://openalex.org/keywords/protonation","display_name":"Protonation","score":0.6560140252113342},{"id":"https://openalex.org/keywords/free-energy-perturbation","display_name":"Free energy perturbation","score":0.5969213247299194},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.584485650062561},{"id":"https://openalex.org/keywords/d-amino-acid-oxidase","display_name":"D-amino acid oxidase","score":0.5488144755363464},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.5168405175209045},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.48698171973228455},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.45217353105545044},{"id":"https://openalex.org/keywords/oxidase-test","display_name":"Oxidase test","score":0.3042322099208832},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.19214275479316711},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.13769319653511047},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.12777969241142273}],"concepts":[{"id":"https://openalex.org/C2780591553","wikidata":"https://www.wikidata.org/wiki/Q417106","display_name":"Indazole","level":2,"score":0.8520257472991943},{"id":"https://openalex.org/C2781269603","wikidata":"https://www.wikidata.org/wiki/Q899683","display_name":"Isoxazole","level":2,"score":0.8380545377731323},{"id":"https://openalex.org/C111233374","wikidata":"https://www.wikidata.org/wiki/Q334640","display_name":"Tautomer","level":2,"score":0.8280671238899231},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.819334864616394},{"id":"https://openalex.org/C30095370","wikidata":"https://www.wikidata.org/wiki/Q899488","display_name":"Protonation","level":3,"score":0.6560140252113342},{"id":"https://openalex.org/C162641036","wikidata":"https://www.wikidata.org/wiki/Q5500215","display_name":"Free energy perturbation","level":3,"score":0.5969213247299194},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.584485650062561},{"id":"https://openalex.org/C2778239910","wikidata":"https://www.wikidata.org/wiki/Q24785797","display_name":"D-amino acid oxidase","level":4,"score":0.5488144755363464},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.5168405175209045},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.48698171973228455},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.45217353105545044},{"id":"https://openalex.org/C38485361","wikidata":"https://www.wikidata.org/wiki/Q576379","display_name":"Oxidase test","level":3,"score":0.3042322099208832},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.19214275479316711},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.13769319653511047},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.12777969241142273},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.0},{"id":"https://openalex.org/C185544564","wikidata":"https://www.wikidata.org/wiki/Q81197","display_name":"Nuclear physics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003605","descriptor_name":"D-Amino-Acid Oxidase","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D003605","descriptor_name":"D-Amino-Acid Oxidase","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D003605","descriptor_name":"D-Amino-Acid Oxidase","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007191","descriptor_name":"Indazoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007191","descriptor_name":"Indazoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007191","descriptor_name":"Indazoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-018-0097-y","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-018-0097-y","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:29335871","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29335871","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 computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8299999833106995}],"awards":[{"id":"https://openalex.org/G2241766024","display_name":null,"funder_award_id":"K111862","funder_id":"https://openalex.org/F4320321994","funder_display_name":"Hungarian Scientific Research Fund"}],"funders":[{"id":"https://openalex.org/F4320321994","display_name":"Hungarian Scientific Research Fund","ror":"https://ror.org/00v349e63"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1973081932","https://openalex.org/W1987275960","https://openalex.org/W1992688758","https://openalex.org/W1994714350","https://openalex.org/W2020451388","https://openalex.org/W2029932670","https://openalex.org/W2043232646","https://openalex.org/W2046106956","https://openalex.org/W2064873310","https://openalex.org/W2086922322","https://openalex.org/W2088790808","https://openalex.org/W2090907772","https://openalex.org/W2121683187","https://openalex.org/W2124357718","https://openalex.org/W2130479394","https://openalex.org/W2141883369","https://openalex.org/W2144627230","https://openalex.org/W2154670681","https://openalex.org/W2176553778","https://openalex.org/W2192077254","https://openalex.org/W2222589778","https://openalex.org/W2302259445","https://openalex.org/W2323942455","https://openalex.org/W2326325773","https://openalex.org/W2404459885","https://openalex.org/W2554947919","https://openalex.org/W2597025763"],"related_works":["https://openalex.org/W2949761423","https://openalex.org/W2068086627","https://openalex.org/W2144975859","https://openalex.org/W2950112971","https://openalex.org/W2050445366","https://openalex.org/W4236672925","https://openalex.org/W2056929289","https://openalex.org/W2062958690","https://openalex.org/W2037177127","https://openalex.org/W2339162320"],"abstract_inverted_index":null,"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
