WATsite: Hydration site prediction program with PyMOL interface
نویسندگان
چکیده
منابع مشابه
Ligand-based virtual screening interface between PyMOL and LiSiCA
Ligand-based virtual screening of large small-molecule databases is an important step in the early stages of drug development. It is based on the similarity principle and is used to reduce the chemical space of large databases to a manageable size where chosen ligands can be experimentally tested. Ligand-based virtual screening can also be used to identify bioactive molecules with different bas...
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Water contributes significantly to the binding of small molecules to proteins in biochemical systems. Molecular dynamics (MD) simulation based programs such as WaterMap and WATsite have been used to probe the locations and thermodynamic properties of hydration sites at the surface or in the binding site of proteins generating important information for structure-based drug design. However, quest...
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When performing physical work, sweat output often exceeds water intake, producing a body water deficit or dehydration. Specific to the work place, dehydration can adversely affect worker productivity, safety, and morale. Legislative bodies in North America such as the Occupational Safety and Health Administration (OSHA) and the American Conference of Governmental Industrial Hygienists (ACGIH) r...
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Docking of small molecule compounds into the binding site of a receptor and estimating the binding affinity of the complex is an important part of the structure-based drug design process. For a thorough understanding of the structural principles that determine the strength of a protein/ligand complex both, an accurate and fast docking protocol and the ability to visualize binding geometries and...
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Water is often found to mediate interactions between a ligand and a protein. It can play a significant role in orientating the ligand within a binding pocket and contribute to the free energy of binding. It would thus be extremely useful to be able to accurately predict the position and orientation of water molecules within a binding pocket. Recently, we developed the WaterDock protocol that wa...
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ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2014
ISSN: 0192-8651
DOI: 10.1002/jcc.23616