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Title: A Multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors
Author: Granadino Roldán, José M.
Garzón, Andrés
Gómez Gutiérrez, Patrícia
Pasamontes Funes, Ignacio
Tomás Belenguer, Maria Santos
Rubio Martínez, Jaime
Keywords: Disseny de medicaments
Proteïnes supressores de tumors
Drug design
Tumor suppressor protein
Issue Date: 17-Jan-2018
Publisher: Future Science
Abstract: 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.
Note: Versió postprint del document publicat a:
It is part of: Future Medicinal Chemistry, 2018, vol. 10, p. 297-318
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ISSN: 1756-8919
Appears in Collections:Articles publicats en revistes (Ciència dels Materials i Química Física)
Articles publicats en revistes (Institut de Química Teòrica i Computacional (IQTCUB))

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