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- Title
WATCLUST: a tool for improving the design of drugs based on protein-water interactions.
- Authors
Ló pez, Elias D.; Arcon, Juan Pablo; Gauto, Diego F.; Petruk, Ariel A.; Modenutti, Carlos P.; Dumas, Victoria G.; Marti, Marcelo A.; Turjanski, Adrian G.
- Abstract
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/.
- Subjects
MOLECULAR structure of water; PROTEIN folding; MOLECULAR dynamics; LIGAND binding (Biochemistry); DOCUMENTATION
- Publication
Bioinformatics, 2015, Vol 31, Issue 22, p3697
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btv411