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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Autores principales: López, E.D., Arcon, J.P., Gauto, D.F., Petruk, A.A., Modenutti, C.P., Dumas, V.G., Marti, M.A., Turjanski, A.G.
Formato: JOUR
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: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 todo:paper_13674803_v31_n22_p3697_Lopez
record_format dspace
spelling todo:paper_13674803_v31_n22_p3697_Lopez2023-10-03T16:11:33Z WATCLUST: A tool for improving the design of drugs based on protein-water interactions López, E.D. Arcon, J.P. Gauto, D.F. Petruk, A.A. Modenutti, C.P. Dumas, V.G. Marti, M.A. Turjanski, A.G. 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. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar 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
López, E.D.
Arcon, J.P.
Gauto, D.F.
Petruk, A.A.
Modenutti, C.P.
Dumas, V.G.
Marti, M.A.
Turjanski, A.G.
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.
format JOUR
author López, E.D.
Arcon, J.P.
Gauto, D.F.
Petruk, A.A.
Modenutti, C.P.
Dumas, V.G.
Marti, M.A.
Turjanski, A.G.
author_facet López, E.D.
Arcon, J.P.
Gauto, D.F.
Petruk, A.A.
Modenutti, C.P.
Dumas, V.G.
Marti, M.A.
Turjanski, A.G.
author_sort López, E.D.
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
url http://hdl.handle.net/20.500.12110/paper_13674803_v31_n22_p3697_Lopez
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