Characterization of Hydration Properties in Structural Ensembles of Biomolecules

Characterization of Hydration Properties in Structural Ensembles of Biomolecules
Characterization of Hydration Properties in Structural Ensembles of Biomolecules
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Journal of Chemical Information and Modeling
Publication Date:
29 May 2019
J. Chem. Inf. Model. 2019, 59, 7, 3316-3329
Solute-solvent interactions are critical for biomolecular stability and recognition. Explicit solvent molecular dynamics (MD) simulations are routinely used to probe such interactions. However, detailed analyses and interpretation of the hydration patterns seen in MD simulations can be both complex and time-consuming. A variety of approaches/tools to compute and interrogate hydration properties in structural ensembles of proteins, nucleic acids, or in general any molecule are available and are complemented here with a new and free software package ("JAL"). Central to "JAL" is an intuitive atom centric approach of computing hydration properties. In addition to the standard metrics commonly used to understand hydration, "JAL" introduces two nonstandard utilities: a program to rapidly compute buried waters in an MD trajectory and a new method to compute multiwater bridges around a solute. We demonstrate the utility of the package by probing the hydration characteristics of the tumor suppressor protein p53 and the translation initiation factor eif4E. "JAL" is hosted online and can be accessed for free at .
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Funding Info:
M.R.P. was funded by the Research Scholarship Award by Bioinformatics Institute-NTU/SCE Joint Ph.D. Program. M.N.N. would like to thank A*STAR Joint Council Office (JCO) Career Development Award [15302FG145] for support. S.K. is partly funded by IAF-PP grant H18/01/a0/015 (A*STAR/NRF/EDB); S.J.F. is funded by IAF-PP grant H17/01/a0/0W9 (A*STAR/NRF/EDB). Support by the A*STAR Biomedical Research Council (BMRC) and computing facility by A*STAR Computing Resource Centre (A*CRC), Agency for Science Technology and Research (A*STAR), Singapore, and NSCC, Singapore.
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Information and Modeling, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see
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