Bernard Brooks, Ph.D.

Senior Investigator

12 South Dr
Bethesda, MD 20814
United States



Bernard Brooks earned an S.B. in chemistry from Massachussets Institute of Technology in 1975 and a Ph.D. in chemistry from University of California, Berkeley in 1979. He did his postdoctoral at Harvard University under the supervision of the Dr. Martin Karplus and he joined the NIH in 1990 as a staff fellow in the Division of Computer Research and Technology at the National Institutes of Health. In 1998 we become the Chief of Molecular Graphics and Simulation Section of the Laboratory of Structural Biology and in 1998 he occupied the position of Chief of the Computational Biophysics Section of the Laboratory of Biophysical Chemistry of the National Heart, Lung and Blood Institute. Since 2005 he is the Chief of the Laboratory of Computational Biology at the NHLBI. In 2008 he received the NHLBI Oustanding Mentor Award and in 2010 he got the NIH Merit Award in recognition of defining the needs of supercomputing power to meet contemporary scientific needs at NIH.


Research Interests
- Bernard Brooks, Ph.D.

Dr. Brooks' research group have been involved in CHARMM development and oversight for more than 30 years. His research efforts have involved the development of new methods to assist the interpretation of experiment, for integrating multiple computational models into a single (multiscale) computation, the development of methods for normal mode analysis of large bio-macromolecules, new enhanced sampling methods, new restraint methods, and techniques for finding reaction pathways in complex systems. All of these developments are integrated into CHARMM, a complete tool for complementing and enhancing experimental research.

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Selected Publications

A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations.

Authors: Roe DR, Brooks BR.
The Journal of Chemical Physics 2020 Aug 07;153(5):

Psi4 1.4: Open-source software for high-throughput quantum chemistry.

Authors: Smith DGA, Burns LA, Simmonett AC, Parrish RM, Schieber MC, Galvelis R, Kraus P, Kruse H, Di Remigio R, Alenaizan A, James AM, Lehtola S, Misiewicz JP, Scheurer M, Shaw RA, Schriber JB, Xie Y, Glick ZL, Sirianni DA, O'Brien JS, Waldrop JM, Brooks BR
Journal of Chemical Physics 2020 May 14;152(18):

SAMPL6 logP challenge: machine learning and quantum mechanical approaches.

Authors: Patel P, Kuntz DM, Jones MR, Brooks BR, Wilson AK.
Journal of Computer-Aided Molecular Design 2020 May 01;34(5):495-510

Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge.

Authors: Krämer A, Hudson PS, Jones MR, Brooks BR.
Journal of Computer-Aided Molecular Design 2020 May 01;34(5):471-483