Computational Biophysics Section

	An image of an E2CD protein. The laboratory uses advanced modeling and visualization tools in molecular biology simulations.

Bernard Brooks, PhD, Principal Investigator

The research staff of the Computational Biophysics Section (CBS) studies modern problems in Biology and Chemistry by developing, executing, and evaluating the results of computer simulations. This process helps scientists understand a variety of important issues such as how the HIV virus binds to a cell in order to infect it or how a particular drug will affect the human body. The long term goal of the research is to be able to use computers as an equal partner with experiments to facilitate the development and design of therapies, drugs, and treatments for a variety of human pathologies.

To achieve this goal, researchers in the CBS study several different biomolecular systems using a variety of different approaches and actively work on developing and testing new simulation methods. We use both classical and quantum mechanical analysis in our simulations. Recent advances in these techniques now allow the study of the energetic details of protein mechanisms. Our scientists have applied these advances to examine the molecular basis of the reactivity of several enzyme systems. Among our specific areas of research are:

As a necessary part of the CBS's research, we have developed extensive competency with scientific supercomputing. The parent organization of the CBS, the Laboratory of Computational Biology, maintains the LoBoS computer cluster, which CBS researchers utilize. We also have available the NIH Helix systems and the Biowulf cluster. Many CBS scientists actively develop the molecular modeling software that is used by the CBS and at other labs. For example, CBS researchers conduct much of the development of the CHARMM software.

The CBS is led by Dr. Bernard Brooks, who is also the chief of the section's parent organization, the Laboratory of Computational Biology (LCB). The LCB is part of Biochemistry and Biophysics Center of the Division of Intramural Research in the National Heart, Lung, and Blood Institute in the National Institutes of Health.

Selected Publications:

Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations, JOURNAL OF MOLECULAR BIOLOGY, Volume 350, Issue 4, 22 July 2005, pp. 817-829 Stan G, Brooks BR, Thirumalai D

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin, BIOPHYSICS JOURNAL, Volume 89, Number 1, 6 May 2005, pp. 167-178 Zheng W, Brooks BR

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved, STRUCTURE, Volume 13, Issue 4, April 2005, pp. 565-577 Zheng W, Brooks BR, Doniach S, Thirumalai D

An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer, JOURNAL OF PHYSICAL CHEMISTRY B, Volume 109, Issue 11, 24 Mar. 2005, pp. 5300-5311 Klauda JB, Brooks BR, MacKerell AD, Venable RM, Pastor RW

Identification of Dynamical Correlations within the Myosin Motor Domain by the Normal Mode Analysis of an Elastic Network Model, JOURNAL OF MOLECULAR BIOLOGY, Vol 346, Issue 3, 25 Feb. 2005, pp. 745-759, Zheng W, Brooks BR

Isotropic periodic sum: A method for the calcuation of long-range interactions, JOURNAL OF CHEMICAL PHYSICS, Volume 122, Issue 4, 22 Jan. 2005, Article 044107, Wu XW, Brooks BR

View complete list of publications for Laboratory of Computational Biophysics.