Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.
The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high-resolution, three-dimensional grid. The CPPTRAJ implementation, called GIST-cpptraj, has a simple, easy-to-use command line interface, and is open source and freely distributed. We have also developed a set of open-source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST-cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc.
Department of Chemistry, Lehman College, 205 W Bedford Pk Blvd, Bronx, New York, 10468.|Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York, 10016.
Steven
S
Ramsey
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0736.
Crystal
C
Nguyen
San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, California, 92093-0505.
Romelia
R
Salomon-Ferrer
San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, California, 92093-0505.|Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0505.
Ross C
RC
Walker
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0736.
Michael K
MK
Gilson
Department of Chemistry, Lehman College, 205 W Bedford Pk Blvd, Bronx, New York, 10468.|Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York, 10016.|Ph. D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York, 10016.
Tom
T
Kurtzman
D000465:Algorithms; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*; D012995:Solubility; D013499:Surface Properties; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D011506:Proteins; D014867:Water
AMBER; drug design; inhomogeneous fluid solvation theory; molecular recognition; solvation thermodynamics; water