Bernard R Brooks
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Explore the profile of Bernard R Brooks including associated specialties, affiliations and a list of published articles.
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Articles
198
Citations
4572
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Recent Articles
1.
Wu X, Brooks B
Int J Mol Sci
. 2025 Mar;
26(5).
PMID: 40076595
Self-guided (SG) molecular simulation methods, namely self-guided molecular dynamics (SGMD) and self-guided Langevin dynamics (SGLD), enhance conformational search by promoting low-frequency motion. A simple local time averaging scheme is used...
2.
Yehia S, Wang J, Brudvig G, Gunner M, Brooks B, Amin M
Biochim Biophys Acta Bioenerg
. 2024 Dec;
1866(2):149531.
PMID: 39694218
Photosystem II (PSII) is a unique natural catalyst that converts solar energy into chemical energy using earth abundant elements in water at physiological pH. Understanding the reaction mechanism will aid...
3.
Hwang W, Austin S, Blondel A, Boittier E, Boresch S, Buck M, et al.
J Phys Chem B
. 2024 Sep;
128(41):9976-10042.
PMID: 39303207
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in...
4.
Rice A, Prasad S, Brooks B, Pastor R
Methods Enzymol
. 2024 Jul;
701:309-358.
PMID: 39025575
Molecular dynamics (MD) simulations of symmetric lipid bilayers are now well established, while those of asymmetric ones are considerably less developed. This disjunction arises in part because the surface tensions...
5.
Amin M, Brooks B
Biophys J
. 2024 May;
123(12):1648-1653.
PMID: 38733082
DNA primase is an iron sulfur enzyme in DNA replication responsible for synthesizing short RNA primers that serve as starting points for DNA synthesis. The role of the [4Fe-4S] cluster...
6.
Amin M, Kaur D, Brudvig G, Brooks B
J Chem Theory Comput
. 2024 Feb;
20(3):1414-1422.
PMID: 38306696
The oxygen-evolving complex (OEC) of Photosystem II catalyzes the water-splitting reaction using solar energy. Thus, understanding the reaction mechanism will inspire the design of biomimetic artificial catalysts that convert solar...
7.
Roe D, Brooks B
J Comput Chem
. 2023 Dec;
45(10):633-637.
PMID: 38071482
The grid inhomogeneous solvation theory (GIST) method requires the often time-consuming calculation of water-water and water-solute energy on a grid. Previous efforts to speed up this calculation include using OpenMP,...
8.
Ghorbani M, Brooks B, Klauda J
J Phys Chem B
. 2023 Aug;
127(31):6887-6895.
PMID: 37527428
Conformational dynamics in proteins can give rise to aggregation prone states during folding, and these kinetically stable states could form oligomers and aggregates. In this study, we investigate the intermediate...
9.
Chen A, Brooks B, Damjanovic A
Proc Natl Acad Sci U S A
. 2023 Jun;
120(26):e2220343120.
PMID: 37339196
In bacterial voltage-gated sodium channels, the passage of ions through the pore is controlled by a selectivity filter (SF) composed of four glutamate residues. The mechanism of selectivity has been...
10.
Roe D, Brooks B
Protein Sci
. 2022 Nov;
31(12):e4511.
PMID: 36382864
Molecular dynamics (MD) simulations are now able to routinely reach timescales of microseconds and beyond. This has led to a corresponding increase in the amount of MD trajectory data that...