WATCLUST: A tool for improving the design of drugs based on protein-water interactions

Motivation: Water molecules are key players for protein folding and function. On the protein surface, water is not placed randomly, but display instead a particular structure evidenced by the presence of specific water sites (WS). These WS can be derived and characterized using explicit water Molecu...

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Detalles Bibliográficos
Autores principales:	Gauto, Diego Fernando, Petruk, Ariel Alcides, Dumas, Victoria Gisel, Martí, Marcelo Adrián, Turjanski, Adrián Gustavo
Publicado:	2015
Materias:	Escherichia coli protein protein water chemistry computer program drug design molecular dynamics Drug Design Escherichia coli Proteins Molecular Dynamics Simulation Proteins Software Water
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v31_n22_p3697_Lopez http://hdl.handle.net/20.500.12110/paper_13674803_v31_n22_p3697_Lopez
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_13674803_v31_n22_p3697_Lopez
record_format	dspace
spelling	paper:paper_13674803_v31_n22_p3697_Lopez2023-06-08T16:12:10Z WATCLUST: A tool for improving the design of drugs based on protein-water interactions Gauto, Diego Fernando Petruk, Ariel Alcides Dumas, Victoria Gisel Martí, Marcelo Adrián Turjanski, Adrián Gustavo Escherichia coli protein protein water chemistry computer program drug design molecular dynamics Drug Design Escherichia coli Proteins Molecular Dynamics Simulation Proteins Software Water Motivation: Water molecules are key players for protein folding and function. On the protein surface, water is not placed randomly, but display instead a particular structure evidenced by the presence of specific water sites (WS). These WS can be derived and characterized using explicit water Molecular Dynamics simulations, providing useful information for ligand binding prediction and design. Here we present WATCLUST, a WS determination and analysis tool running on the VMD platform. The tool also allows direct transfer of the WS information to Autodock program to perform biased docking. Availability and implementation: The WATCLUST plugin and documentation are freely available at http://sbg.qb.fcen.uba.ar/watclust/. © The Author 2015. Published by Oxford University Press. All rights reserved. Fil:Gauto, D.F. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Petruk, A.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Dumas, V.G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Marti, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Turjanski, A.G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2015 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v31_n22_p3697_Lopez http://hdl.handle.net/20.500.12110/paper_13674803_v31_n22_p3697_Lopez
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Escherichia coli protein protein water chemistry computer program drug design molecular dynamics Drug Design Escherichia coli Proteins Molecular Dynamics Simulation Proteins Software Water
spellingShingle	Escherichia coli protein protein water chemistry computer program drug design molecular dynamics Drug Design Escherichia coli Proteins Molecular Dynamics Simulation Proteins Software Water Gauto, Diego Fernando Petruk, Ariel Alcides Dumas, Victoria Gisel Martí, Marcelo Adrián Turjanski, Adrián Gustavo WATCLUST: A tool for improving the design of drugs based on protein-water interactions
topic_facet	Escherichia coli protein protein water chemistry computer program drug design molecular dynamics Drug Design Escherichia coli Proteins Molecular Dynamics Simulation Proteins Software Water
description	Motivation: Water molecules are key players for protein folding and function. On the protein surface, water is not placed randomly, but display instead a particular structure evidenced by the presence of specific water sites (WS). These WS can be derived and characterized using explicit water Molecular Dynamics simulations, providing useful information for ligand binding prediction and design. Here we present WATCLUST, a WS determination and analysis tool running on the VMD platform. The tool also allows direct transfer of the WS information to Autodock program to perform biased docking. Availability and implementation: The WATCLUST plugin and documentation are freely available at http://sbg.qb.fcen.uba.ar/watclust/. © The Author 2015. Published by Oxford University Press. All rights reserved.
author	Gauto, Diego Fernando Petruk, Ariel Alcides Dumas, Victoria Gisel Martí, Marcelo Adrián Turjanski, Adrián Gustavo
author_facet	Gauto, Diego Fernando Petruk, Ariel Alcides Dumas, Victoria Gisel Martí, Marcelo Adrián Turjanski, Adrián Gustavo
author_sort	Gauto, Diego Fernando
title	WATCLUST: A tool for improving the design of drugs based on protein-water interactions
title_short	WATCLUST: A tool for improving the design of drugs based on protein-water interactions
title_full	WATCLUST: A tool for improving the design of drugs based on protein-water interactions
title_fullStr	WATCLUST: A tool for improving the design of drugs based on protein-water interactions
title_full_unstemmed	WATCLUST: A tool for improving the design of drugs based on protein-water interactions
title_sort	watclust: a tool for improving the design of drugs based on protein-water interactions
publishDate	2015
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v31_n22_p3697_Lopez http://hdl.handle.net/20.500.12110/paper_13674803_v31_n22_p3697_Lopez
work_keys_str_mv	AT gautodiegofernando watclustatoolforimprovingthedesignofdrugsbasedonproteinwaterinteractions AT petrukarielalcides watclustatoolforimprovingthedesignofdrugsbasedonproteinwaterinteractions AT dumasvictoriagisel watclustatoolforimprovingthedesignofdrugsbasedonproteinwaterinteractions AT martimarceloadrian watclustatoolforimprovingthedesignofdrugsbasedonproteinwaterinteractions AT turjanskiadriangustavo watclustatoolforimprovingthedesignofdrugsbasedonproteinwaterinteractions
_version_	1768546316164530176

WATCLUST: A tool for improving the design of drugs based on protein-water interactions

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