MobyWat is a program for analysis and prediction of hydration structure of molecular surfaces and interfaces. The program uses a series of frames sampled from molecular simulations performed with explicit water models.
http://www.mobywat.com/
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MobyWat - SCOPE | mobywat.com Reviews
https://mobywat.com
MobyWat is a program for analysis and prediction of hydration structure of molecular surfaces and interfaces. The program uses a series of frames sampled from molecular simulations performed with explicit water models.
mobywat.com
MobyWat - ABOUT
http://www.mobywat.com/index.php/about
MobyWat calculates the hydration structure of a molecular surface (I) and/or an interface (II). Matches between experimental (red) and MobyWat (blue) positions of water oxygen atoms. Hydration network of a molecular interface can be calculated by the NetDraw mode of MobyWat. Hydration network of a molecular surface can be calculated by the NetDraw mode of MobyWat. Joomla gallery extension by joomlashine.com. MobyWat calculates the hydration structure of a molecular surface (I) and/or an interface (II).
MobyWat - Glossary
http://www.mobywat.com/index.php/backgr/glossa
Mobility of water molecules can be followed at an atomic scale by calculation methods such as molecular dynamics. As a result of a molecular dynamics run, spatial positions of all atoms are recorded at regular time steps. The set of coordinates of all atoms recorded after a time step is called a frame. MobyWat predicts hydration of the surface (SF) of a single solute molecule (target) or the interface (IF) of a target-ligand complex. Tests of SF predictions were published ( Jeszenői et al. 2015a. A joint...
MobyWat - Program details
http://www.mobywat.com/index.php/about/pdetails
1 Organization of code. Fig PD1: Main connections and I/O flow in MobyWat source code. 2 Water pool data type. MobyWat uses a pool list with spatial coordinates, atom- and residue serial numbers of oxygen atoms for identification of a water molecule in the pool (Fig. PD2). The binary pool waters file. Stores pool lists of all selected waters and all frames specified at command line. Besides the benefits of shorter repeated runs, creation of plw files allows efficient use of disk space and memory.
MobyWat - File types
http://www.mobywat.com/index.php/module-styles/file-types
The present version of MobyWat accepts four types of structural input files. File types are automatically recognized by extensions of file names. 11 Binary trajectory file (*.xtc). The xtc format is a portable binary format which can store trajectories in an efficient, compressed form. It uses the xdr routines for writing and reading data. Xtc files can be produced by e.g. MD package GROMACS. Along with the production of the xtc file in GROMACS. 12 Separate PDB files (*.pdb). It is important to note that...
MobyWat - Input parameters
http://www.mobywat.com/index.php/module-styles/params
Required formats and default values of numerical and alphabetical parameters are listed e.g. in the quick help which can be printed to the screen by typing the name of the program at the command prompt:.
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MobyWat - SCOPE
MobyWat calculates the hydration structure of a molecular surface (I) and/or an interface (II). Matches between experimental (red) and MobyWat (blue) positions of water oxygen atoms. Hydration network of a molecular interface can be calculated by the NetDraw mode of MobyWat. Hydration network of a molecular surface can be calculated by the NetDraw mode of MobyWat. Joomla gallery extension by joomlashine.com. MobyWat calculates the hydration structure of a molecular surface (I) and/or an interface (II).
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