{"id":"https://openalex.org/W1996690269","doi":"https://doi.org/10.1021/ci5005256","title":"VAMMPIRE-LORD: A Web Server for Straightforward Lead Optimization Using Matched Molecular Pairs","display_name":"VAMMPIRE-LORD: A Web Server for Straightforward Lead Optimization Using Matched Molecular Pairs","publication_year":2015,"publication_date":"2015-01-28","ids":{"openalex":"https://openalex.org/W1996690269","doi":"https://doi.org/10.1021/ci5005256","mag":"1996690269","pmid":"https://pubmed.ncbi.nlm.nih.gov/25629725"},"language":"en","primary_location":{"id":"doi:10.1021/ci5005256","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci5005256","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/A5088572698","display_name":"J\u00falia W\u00e9ber","orcid":"https://orcid.org/0000-0002-0510-5106"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Julia Weber","raw_affiliation_strings":["Institute of Pharmaceutical\rChemistry, Goethe University, Frankfurt 60438, Germany","Institute of Pharmaceutical Chemistry, Goethe University , Frankfurt 60438, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmaceutical\rChemistry, Goethe University, Frankfurt 60438, Germany","institution_ids":["https://openalex.org/I114090438"]},{"raw_affiliation_string":"Institute of Pharmaceutical Chemistry, Goethe University , Frankfurt 60438, Germany","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064516687","display_name":"Janosch Achenbach","orcid":"https://orcid.org/0000-0001-9712-1471"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Janosch Achenbach","raw_affiliation_strings":["Institute of Pharmaceutical\rChemistry, Goethe University, Frankfurt 60438, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmaceutical\rChemistry, Goethe University, Frankfurt 60438, Germany","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080626003","display_name":"Daniel Moser","orcid":"https://orcid.org/0000-0002-3457-6759"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Daniel Moser","raw_affiliation_strings":["Institute of Pharmaceutical\rChemistry, Goethe University, Frankfurt 60438, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmaceutical\rChemistry, Goethe University, Frankfurt 60438, Germany","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002124394","display_name":"Ewgenij Proschak","orcid":"https://orcid.org/0000-0003-1961-1859"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ewgenij Proschak","raw_affiliation_strings":["Institute of Pharmaceutical\rChemistry, Goethe University, Frankfurt 60438, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmaceutical\rChemistry, Goethe University, Frankfurt 60438, Germany","institution_ids":["https://openalex.org/I114090438"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5002124394"],"corresponding_institution_ids":["https://openalex.org/I114090438"],"apc_list":null,"apc_paid":null,"fwci":2.9076,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.91118297,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"55","issue":"2","first_page":"207","last_page":"213"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9894999861717224,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/lead","display_name":"Lead (geology)","score":0.7244719862937927},{"id":"https://openalex.org/keywords/web-site","display_name":"Web site","score":0.5618724822998047},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.547149121761322},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5075027346611023},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4232778251171112},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33620887994766235},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23009192943572998},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.22342687845230103}],"concepts":[{"id":"https://openalex.org/C2777093003","wikidata":"https://www.wikidata.org/wiki/Q6508345","display_name":"Lead (geology)","level":2,"score":0.7244719862937927},{"id":"https://openalex.org/C2984519610","wikidata":"https://www.wikidata.org/wiki/Q35127","display_name":"Web site","level":3,"score":0.5618724822998047},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.547149121761322},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5075027346611023},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4232778251171112},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33620887994766235},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23009192943572998},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.22342687845230103},{"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":"D005544","descriptor_name":"Forecasting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005544","descriptor_name":"Forecasting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005544","descriptor_name":"Forecasting","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D020407","descriptor_name":"Internet","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D052246","descriptor_name":"Cyclooxygenase 2 Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D052246","descriptor_name":"Cyclooxygenase 2 Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D052246","descriptor_name":"Cyclooxygenase 2 Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D052246","descriptor_name":"Cyclooxygenase 2 Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D052246","descriptor_name":"Cyclooxygenase 2 Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D052246","descriptor_name":"Cyclooxygenase 2 Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000295","qualifier_name":"instrumentation","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":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci5005256","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci5005256","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:25629725","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25629725","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/G2239574037","display_name":null,"funder_award_id":"PR 1405/2-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G3541115506","display_name":null,"funder_award_id":"SFB 1039 A07","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1835740130","https://openalex.org/W1972156862","https://openalex.org/W1993046136","https://openalex.org/W2001284100","https://openalex.org/W2005518172","https://openalex.org/W2013085020","https://openalex.org/W2014678042","https://openalex.org/W2024289521","https://openalex.org/W2032998352","https://openalex.org/W2033498682","https://openalex.org/W2034122948","https://openalex.org/W2039831563","https://openalex.org/W2057898340","https://openalex.org/W2058015994","https://openalex.org/W2065651723","https://openalex.org/W2068171522","https://openalex.org/W2071302369","https://openalex.org/W2087952495","https://openalex.org/W2088970363","https://openalex.org/W2130479394","https://openalex.org/W2132802776","https://openalex.org/W2143000571","https://openalex.org/W2275300015","https://openalex.org/W2323605167","https://openalex.org/W2329862012","https://openalex.org/W2401258374"],"related_works":["https://openalex.org/W255623911","https://openalex.org/W291827334","https://openalex.org/W1601617767","https://openalex.org/W2766007331","https://openalex.org/W2027911892","https://openalex.org/W2520355961","https://openalex.org/W1606752009","https://openalex.org/W4245697572","https://openalex.org/W277486614","https://openalex.org/W2419063854"],"abstract_inverted_index":{"VAMMPIRE-LORD":[0,101],"(lead":[1],"optimization":[2,115],"by":[3],"rational":[4],"design)":[5],"describes":[6],"an":[7],"innovative":[8],"strategy":[9],"to":[10,82,97],"improve":[11],"the":[12,55,59,77,84,91,110,114],"binding":[13],"affinity":[14,96],"of":[15,31,86,117],"a":[16,42,48,62,67,87,105,118],"defined":[17,28,119],"lead":[18,120],"compound":[19],"using":[20],"3D":[21],"matched":[22],"molecular":[23],"pairs":[24,30],"(3D-MMPs).":[25],"3D-MMPs":[26],"are":[27],"as":[29,58,104],"molecules":[32],"that":[33,53,76,108],"differ":[34],"in":[35],"exactly":[36],"one":[37],"structural":[38],"transformation":[39,64,89],"and":[40,65,90],"have":[41],"known":[43],"bioactive":[44],"conformation.":[45],"We":[46,74],"developed":[47],"novel":[49],"atom-pair":[50],"descriptor":[51],"(LORD_FP)":[52],"represents":[54],"ligand-as":[56],"well":[57],"receptor":[60],"environment-of":[61],"chemical":[63,88],"built":[66],"predictive":[68],"model":[69,79],"based":[70],"on":[71,94],"17602":[72],"3D-MMPs.":[73],"demonstrate":[75],"created":[78],"is":[80],"able":[81],"extrapolate":[83],"knowledge":[85],"associated":[92],"effect":[93],"ligand":[95],"any":[98],"similar":[99],"system.":[100],"was":[102],"implemented":[103],"web":[106],"server":[107],"guides":[109],"user":[111],"step-by-step":[112],"through":[113],"process":[116],"compound.":[121]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}