Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds
- Autores
- Scardino, Valeria; Bollini, Mariela; Cavasotto, Claudio Norberto
- Año de publicación
- 2021
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- The use of high-throughput docking (HTD) in the drug discovery pipeline is today widely established. In spite of methodological improvements in docking accuracy (pose prediction), scoring power, ranking power, and screening power in HTD remain challenging. In fact, pose prediction is of critical importance in view of the pose-dependent scoring process, since incorrect poses will necessarily decrease the ranking power of scoring functions. The combination of results from different docking programs (consensus scoring) has been shown to improve the performance of HTD. Moreover, it has been also shown that a pose consensus approach might also result in database enrichment. We present a new methodology named Pose/Ranking Consensus (PRC) that combines both pose and ranking consensus approaches, to overcome the limitations of each stand-alone strategy. This approach has been developed using four docking programs (ICM, rDock, Auto Dock 4, and PLANTS; the first one is commercial, the other three are free). We undertook a thorough analysis for the best way of combining pose and rank strategies, and applied the PRC to a wide range of 34 targets sampling different protein families and binding site properties. Our approach exhibits an improved systematic performance in terms of enrichment factor and hit rate with respect to either pose consensus or consensus ranking alone strategies at a lower computational cost, while always ensuring the recovery of a suitable number of ligands. An analysis using four free docking programs (replacing ICM by Auto Dock Vina) displayed comparable results.
Fil: Scardino, Valeria. Universidad Austral; Argentina
Fil: Bollini, Mariela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; Argentina
Fil: Cavasotto, Claudio Norberto. Universidad Austral. Facultad de Ciencias Biomédicas. Instituto de Investigaciones en Medicina Traslacional. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Medicina Traslacional; Argentina - Materia
-
pose and rank consensus
virttual screening - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/173147
Ver los metadatos del registro completo
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oai:ri.conicet.gov.ar:11336/173147 |
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Combination of pose and rank consensus in docking-based virtual screening: The best of both worldsScardino, ValeriaBollini, MarielaCavasotto, Claudio Norbertopose and rank consensusvirttual screeninghttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1The use of high-throughput docking (HTD) in the drug discovery pipeline is today widely established. In spite of methodological improvements in docking accuracy (pose prediction), scoring power, ranking power, and screening power in HTD remain challenging. In fact, pose prediction is of critical importance in view of the pose-dependent scoring process, since incorrect poses will necessarily decrease the ranking power of scoring functions. The combination of results from different docking programs (consensus scoring) has been shown to improve the performance of HTD. Moreover, it has been also shown that a pose consensus approach might also result in database enrichment. We present a new methodology named Pose/Ranking Consensus (PRC) that combines both pose and ranking consensus approaches, to overcome the limitations of each stand-alone strategy. This approach has been developed using four docking programs (ICM, rDock, Auto Dock 4, and PLANTS; the first one is commercial, the other three are free). We undertook a thorough analysis for the best way of combining pose and rank strategies, and applied the PRC to a wide range of 34 targets sampling different protein families and binding site properties. Our approach exhibits an improved systematic performance in terms of enrichment factor and hit rate with respect to either pose consensus or consensus ranking alone strategies at a lower computational cost, while always ensuring the recovery of a suitable number of ligands. An analysis using four free docking programs (replacing ICM by Auto Dock Vina) displayed comparable results.Fil: Scardino, Valeria. Universidad Austral; ArgentinaFil: Bollini, Mariela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; ArgentinaFil: Cavasotto, Claudio Norberto. Universidad Austral. Facultad de Ciencias Biomédicas. Instituto de Investigaciones en Medicina Traslacional. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Medicina Traslacional; ArgentinaRoyal Society of Chemistry2021-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/173147Scardino, Valeria; Bollini, Mariela; Cavasotto, Claudio Norberto; Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds; Royal Society of Chemistry; RSC Advances; 11; 56; 10-2021; 35383-353912046-2069CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1039/d1ra05785einfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:24:21Zoai:ri.conicet.gov.ar:11336/173147instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:24:22.044CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds |
title |
Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds |
spellingShingle |
Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds Scardino, Valeria pose and rank consensus virttual screening |
title_short |
Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds |
title_full |
Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds |
title_fullStr |
Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds |
title_full_unstemmed |
Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds |
title_sort |
Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds |
dc.creator.none.fl_str_mv |
Scardino, Valeria Bollini, Mariela Cavasotto, Claudio Norberto |
author |
Scardino, Valeria |
author_facet |
Scardino, Valeria Bollini, Mariela Cavasotto, Claudio Norberto |
author_role |
author |
author2 |
Bollini, Mariela Cavasotto, Claudio Norberto |
author2_role |
author author |
dc.subject.none.fl_str_mv |
pose and rank consensus virttual screening |
topic |
pose and rank consensus virttual screening |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.4 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
The use of high-throughput docking (HTD) in the drug discovery pipeline is today widely established. In spite of methodological improvements in docking accuracy (pose prediction), scoring power, ranking power, and screening power in HTD remain challenging. In fact, pose prediction is of critical importance in view of the pose-dependent scoring process, since incorrect poses will necessarily decrease the ranking power of scoring functions. The combination of results from different docking programs (consensus scoring) has been shown to improve the performance of HTD. Moreover, it has been also shown that a pose consensus approach might also result in database enrichment. We present a new methodology named Pose/Ranking Consensus (PRC) that combines both pose and ranking consensus approaches, to overcome the limitations of each stand-alone strategy. This approach has been developed using four docking programs (ICM, rDock, Auto Dock 4, and PLANTS; the first one is commercial, the other three are free). We undertook a thorough analysis for the best way of combining pose and rank strategies, and applied the PRC to a wide range of 34 targets sampling different protein families and binding site properties. Our approach exhibits an improved systematic performance in terms of enrichment factor and hit rate with respect to either pose consensus or consensus ranking alone strategies at a lower computational cost, while always ensuring the recovery of a suitable number of ligands. An analysis using four free docking programs (replacing ICM by Auto Dock Vina) displayed comparable results. Fil: Scardino, Valeria. Universidad Austral; Argentina Fil: Bollini, Mariela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; Argentina Fil: Cavasotto, Claudio Norberto. Universidad Austral. Facultad de Ciencias Biomédicas. Instituto de Investigaciones en Medicina Traslacional. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones en Medicina Traslacional; Argentina |
description |
The use of high-throughput docking (HTD) in the drug discovery pipeline is today widely established. In spite of methodological improvements in docking accuracy (pose prediction), scoring power, ranking power, and screening power in HTD remain challenging. In fact, pose prediction is of critical importance in view of the pose-dependent scoring process, since incorrect poses will necessarily decrease the ranking power of scoring functions. The combination of results from different docking programs (consensus scoring) has been shown to improve the performance of HTD. Moreover, it has been also shown that a pose consensus approach might also result in database enrichment. We present a new methodology named Pose/Ranking Consensus (PRC) that combines both pose and ranking consensus approaches, to overcome the limitations of each stand-alone strategy. This approach has been developed using four docking programs (ICM, rDock, Auto Dock 4, and PLANTS; the first one is commercial, the other three are free). We undertook a thorough analysis for the best way of combining pose and rank strategies, and applied the PRC to a wide range of 34 targets sampling different protein families and binding site properties. Our approach exhibits an improved systematic performance in terms of enrichment factor and hit rate with respect to either pose consensus or consensus ranking alone strategies at a lower computational cost, while always ensuring the recovery of a suitable number of ligands. An analysis using four free docking programs (replacing ICM by Auto Dock Vina) displayed comparable results. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-10 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/173147 Scardino, Valeria; Bollini, Mariela; Cavasotto, Claudio Norberto; Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds; Royal Society of Chemistry; RSC Advances; 11; 56; 10-2021; 35383-35391 2046-2069 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/173147 |
identifier_str_mv |
Scardino, Valeria; Bollini, Mariela; Cavasotto, Claudio Norberto; Combination of pose and rank consensus in docking-based virtual screening: The best of both worlds; Royal Society of Chemistry; RSC Advances; 11; 56; 10-2021; 35383-35391 2046-2069 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/doi/10.1039/d1ra05785e |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Royal Society of Chemistry |
publisher.none.fl_str_mv |
Royal Society of Chemistry |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
reponame_str |
CONICET Digital (CONICET) |
collection |
CONICET Digital (CONICET) |
instname_str |
Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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1844614240270286848 |
score |
13.070432 |