A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors

AIM:Rescoring of docking-binding poses can significantly improve molecular docking results. Our aim was to evaluate postprocessing docking protocols in order to determine the most suitable methodology for the study of the binding of congeneric compounds to protein kinases. MATERIALS & METHODS:Di...

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Detalles Bibliográficos
Autores: Granadino Roldán, José M., Garzón Ruiz, Andrés, Pasamontes Funez, Ignacio, Tomás Belenguer, María Santos|||0000-0003-2493-0977, Rubio Martínez, Jaime
Tipo de recurso: artículo
Fecha de publicación:2018
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/113760
Acceso en línea:https://hdl.handle.net/2117/113760
https://dx.doi.org/10.4155/fmc-2017-0156
Access Level:acceso abierto
Palabra clave:Molecules -- Models
B-Raf
MMPB(GB)SA
C-Abl
Docking
P38a
Scoring
Molècules -- Models
Àrees temàtiques de la UPC::Enginyeria química::Química física::Estructura molecular
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repository_id_str
spelling A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitorsGranadino Roldán, José M.Garzón Ruiz, AndrésPasamontes Funez, IgnacioTomás Belenguer, María Santos|||0000-0003-2493-0977Rubio Martínez, JaimeMolecules -- ModelsB-RafMMPB(GB)SAC-AblDockingP38aScoringMolècules -- ModelsÀrees temàtiques de la UPC::Enginyeria química::Química física::Estructura molecularAIM:Rescoring of docking-binding poses can significantly improve molecular docking results. Our aim was to evaluate postprocessing docking protocols in order to determine the most suitable methodology for the study of the binding of congeneric compounds to protein kinases. MATERIALS & METHODS:Diverse ligand-receptor poses generated after docking were submitted to different relaxation protocols. The Molecular Mechanics Poisson-Boltzmann (Generalized Born) Surface Area approach was applied for the evaluation of the binding affinity of complexes obtained. The performance of various Molecular Mechanics Poisson-Boltzmann (Generalized Born) Surface Area methodologies was compared. RESULTS:The inclusion of a postprocessing protocol after docking enhances the quality of the results, although the best methodology is system dependent. CONCLUSION:An examination of the interactions established has allowed us to suggest useful modifications for the design of new type II inhibitors.20182018-01-1720182018-02-05journal articlehttp://purl.org/coar/resource_type/c_6501AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/113760https://dx.doi.org/10.4155/fmc-2017-0156reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivs 3.0 Spainhttp://creativecommons.org/licenses/by-nc-nd/3.0/es/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/1137602026-05-27T15:37:01Z
dc.title.none.fl_str_mv A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
title A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
spellingShingle A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
Granadino Roldán, José M.
Molecules -- Models
B-Raf
MMPB(GB)SA
C-Abl
Docking
P38a
Scoring
Molècules -- Models
Àrees temàtiques de la UPC::Enginyeria química::Química física::Estructura molecular
title_short A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
title_full A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
title_fullStr A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
title_full_unstemmed A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
title_sort A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
dc.creator.none.fl_str_mv Granadino Roldán, José M.
Garzón Ruiz, Andrés
Pasamontes Funez, Ignacio
Tomás Belenguer, María Santos|||0000-0003-2493-0977
Rubio Martínez, Jaime
author Granadino Roldán, José M.
author_facet Granadino Roldán, José M.
Garzón Ruiz, Andrés
Pasamontes Funez, Ignacio
Tomás Belenguer, María Santos|||0000-0003-2493-0977
Rubio Martínez, Jaime
author_role author
author2 Garzón Ruiz, Andrés
Pasamontes Funez, Ignacio
Tomás Belenguer, María Santos|||0000-0003-2493-0977
Rubio Martínez, Jaime
author2_role author
author
author
author
dc.subject.none.fl_str_mv Molecules -- Models
B-Raf
MMPB(GB)SA
C-Abl
Docking
P38a
Scoring
Molècules -- Models
Àrees temàtiques de la UPC::Enginyeria química::Química física::Estructura molecular
topic Molecules -- Models
B-Raf
MMPB(GB)SA
C-Abl
Docking
P38a
Scoring
Molècules -- Models
Àrees temàtiques de la UPC::Enginyeria química::Química física::Estructura molecular
description AIM:Rescoring of docking-binding poses can significantly improve molecular docking results. Our aim was to evaluate postprocessing docking protocols in order to determine the most suitable methodology for the study of the binding of congeneric compounds to protein kinases. MATERIALS & METHODS:Diverse ligand-receptor poses generated after docking were submitted to different relaxation protocols. The Molecular Mechanics Poisson-Boltzmann (Generalized Born) Surface Area approach was applied for the evaluation of the binding affinity of complexes obtained. The performance of various Molecular Mechanics Poisson-Boltzmann (Generalized Born) Surface Area methodologies was compared. RESULTS:The inclusion of a postprocessing protocol after docking enhances the quality of the results, although the best methodology is system dependent. CONCLUSION:An examination of the interactions established has allowed us to suggest useful modifications for the design of new type II inhibitors.
publishDate 2018
dc.date.none.fl_str_mv 2018
2018-01-17
2018
2018-02-05
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
AM
http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/113760
https://dx.doi.org/10.4155/fmc-2017-0156
url https://hdl.handle.net/2117/113760
https://dx.doi.org/10.4155/fmc-2017-0156
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 3.0 Spain
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 3.0 Spain
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,301603

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