Bernard R Brooks

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 17

Top Topics

Diffusion Weighted Imaging

Molecular Dynamics

Metal Organic Framework

Top Venues

The journal of physical chemistry. B

Journal of chemical theory and computation

Journal of computer-aided molecular design

The Journal of chemical physics

This page only lists publications with an associated author ORCID identifier.

Publications

Muhamed Amin, Divya Kaur, Gary W Brudvig, Bernard R Brooks
Mapping the Oxygens in the Oxygen-Evolving Complex of Photosystem II by Their Nucleophilicity Using Quantum Descriptors. Journal of chemical theory and computation 20 (3) (2024)
Muhamed Amin, Divya Kaur, Gary W Brudvig, Bernard R Brooks
Mapping the Oxygens in the Oxygen-Evolving Complex of Photosystem II by Their Nucleophilicity Using Quantum Descriptors. Journal of chemical theory and computation (2024)
Wonmuk Hwang, Steven L Austin, Arnaud Blondel, Eric D Boittier, Stefan Boresch, Matthias Buck, Joshua Buckner, Amedeo Caflisch, Hao-Ting Chang, Xi Cheng, Yeol Kyo Choi, Jhih-Wei Chu, Michael F Crowley, Qiang Cui, Ana Damjanovic, Yuqing Deng, Michael Devereux, Xinqiang Ding, Michael F Feig, Jiali Gao, David R Glowacki, James E Gonzales, Mehdi Bagerhi Hamaneh, Edward D Harder, Ryan L Hayes, Jing Huang, Yandong Huang, Phillip S Hudson, Wonpil Im, Shahidul M Islam, Wei Jiang, Michael R Jones, Silvan Käser, Fiona L Kearns, Nathan R Kern, Jeffery B Klauda, Themis Lazaridis, Jinhyuk Lee, Justin A Lemkul, Xiaorong Liu, Yun Lyna Luo, Alexander D MacKerell, Dan Thomas Major, Markus Meuwly, Kwangho Nam, Lennart Nilsson, Victor Ovchinnikov, Emanuele Paci, Soohyung Park, Richard W Pastor, Amanda R Pittman, Carol Beth Post, Samarjeet Prasad, Jingzhi Pu, John Z H Zhang, Thenmalarchelvi Rathinavelan, Daniel R Roe, Benoı T Roux, Christopher N Rowley, Jana Shen, Andrew C Simmonett, Alexander J Sodt, Kai Töpfer, Meenu Upadhyay, Arjan van der Vaart, Luis Itza Vazquez-Salazar, Richard M Venable, Luke C Warrensford, H Lee Woodcock, Yujin Wu, Charles L Brooks Iii, Bernard R Brooks, Martin Karplus
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The journal of physical chemistry. B (2024)
Ada Y Chen, Juyong Lee, Ana Damjanovic, Bernard R Brooks
Protein p K a Prediction by Tree-Based Machine Learning. Journal of chemical theory and computation 18 (4) (2022)
Yeol Kyo Choi, Nathan R Kern, Seonghan Kim, Krishan Kanhaiya, Yaser Afshar, Sun Hee Jeon, Sunhwan Jo, Bernard R Brooks, Jumin Lee, Ellad B Tadmor, Hendrik Heinz, Wonpil Im
CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems. Journal of chemical theory and computation (2021)
Samarjeet Prasad, Andrew C Simmonett, Rubén Meana-Pañeda, Bernard R Brooks
The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry. Journal of computational chemistry 42 (19) (2021)
Brajesh Narayan, Colm Herbert, Brian J Rodriguez, Bernard R Brooks, Nicolae-Viorel Buchete
Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields. The journal of physical chemistry. B 125 (20) (2021)
Xiongwu Wu, Bernard R Brooks
Reformulation of the self-guided molecular simulation method. The Journal of chemical physics 153 (9) (2020)
Mahdi Ghorbani, Bernard R Brooks, Jeffery B Klauda
Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations. The journal of physical chemistry. B 124 (45) (2020)
Daniel R Roe, Bernard R Brooks
A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations. The Journal of chemical physics 153 (5) (2020)
Rui Tian, Qiao Zeng, Shoujun Zhu, Joseph Lau, Swati Chandra, Robert Ertsey, Kenneth S Hettie, Nutte Tarn Teraphongphom, Zhubin Hu, Gang Niu, Dale O Kiesewetter, Haitao Sun, Xiao-Dong Zhang, Alexander L Antaris, Bernard R Brooks, Xiaoyuan Shawn Chen
Albumin-chaperoned cyanine dye yields superbright NIR-II fluorophore with enhanced pharmacokinetics. Science advances 5 (9) (2019)
Xiongwu Wu, Bernard R Brooks
Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins. The journal of physical chemistry. B 122 (23) (2018)
Phillip S Hudson, Kyungreem Han, H Lee Woodcock, Bernard R Brooks
Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. Journal of computer-aided molecular design 32 (10) (2018)
Naohiro Nishikawa, Kyungreem Han, Xiongwu Wu, Florentina Tofoleanu, Bernard R Brooks
Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges. Journal of computer-aided molecular design 32 (10) (2018)
Bartłomiej Tywoniuk, Ye Yuan, Sarah McCartan, Beata Maria Szydłowska, Florentina Tofoleanu, Bernard R Brooks, Nicolae-Viorel Buchete
Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer's Aβ Protofilaments. The journal of physical chemistry. B 122 (49) (2018)
Kyungreem Han, Phillip S Hudson, Michael R Jones, Naohiro Nishikawa, Florentina Tofoleanu, Bernard R Brooks
Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method. Journal of computer-aided molecular design 32 (10) (2018)
Florentina Tofoleanu, Ye Yuan, Frank C Pickard, Bartłomiej Tywoniuk, Bernard R Brooks, Nicolae-Viorel Buchete
Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations. The journal of physical chemistry. B 122 (21) (2018)