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pro vyhledávání: '"Brooks, Bernard R"'
Finding low dimensional representation of data from long-timescale trajectories of biomolecular processes such as protein-folding or ligand-receptor binding is of fundamental importance and kinetic models such as Markov modeling have proven useful in
Externí odkaz:
http://arxiv.org/abs/2201.04609
Variational embedding of protein folding simulations using gaussian mixture variational autoencoders
Conformational sampling of biomolecules using molecular dynamics simulations often produces large amount of high dimensional data that makes it difficult to interpret using conventional analysis techniques. Dimensionality reduction methods are thus r
Externí odkaz:
http://arxiv.org/abs/2108.12493
Autor:
Amin, Muhamed, Brooks, Bernard R.
Publikováno v:
In Biophysical Journal 18 June 2024 123(12):1648-1653
Publikováno v:
In BBA - Bioenergetics 1 April 2025 1866(2)
We present a new computational approach, Action-CSA, to sample multiple reaction pathways with fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing method. This approach suc
Externí odkaz:
http://arxiv.org/abs/1610.02652
Publikováno v:
Scientific Reports (2017)
We investigate the possibility of global optimization-based overlapping community detection, using link community framework. We first show that partition density, the original quality function used in link community detection method, is not suitable
Externí odkaz:
http://arxiv.org/abs/1601.05100
Publikováno v:
In Biophysical Journal 3 August 2021 120(15):3050-3069
Publikováno v:
In Biophysical Journal 20 July 2021 120(14):2902-2913
Autor:
Roe, Daniel R., Brooks, Bernard R.
Publikováno v:
In Journal of Molecular Graphics and Modelling May 2021 104
Autor:
Hwang, Wonmuk, Austin, Steven L., Blondel, Arnaud, Boittier, Eric D., Boresch, Stefan, Buck, Matthias, Buckner, Joshua, Caflisch, Amedeo, Chang, Hao-Ting, Cheng, Xi, Choi, Yeol Kyo, Chu, Jhih-Wei, Crowley, Michael F., Cui, Qiang, Damjanovic, Ana, Deng, Yuqing, Devereux, Mike, Ding, Xinqiang, Feig, Michael F., Gao, Jiali, Glowacki, David R., Gonzales, James E., Hamaneh, Mehdi Bagerhi, Harder, Edward D., Hayes, Ryan L., Huang, Jing, Huang, Yandong, Hudson, Phillip S., Im, Wonpil, Islam, Shahidul M., Jiang, Wei, Jones, Michael R., Käser, Silvan, Kearns, Fiona L., Kern, Nathan R., Klauda, Jeffery B., Lazaridis, Themis, Lee, Jinhyuk, Lemkul, Justin A., Liu, Xiaorong, Luo, Yun, MacKerell, Alexander D., Major, Dan T., Meuwly, Markus, Nam, Kwangho, Nilsson, Lennart, Ovchinnikov, Victor, Paci, Emanuele, Park, Soohyung, Pastor, Richard W., Pittman, Amanda R., Post, Carol Beth, Prasad, Samarjeet, Pu, Jingzhi, Qi, Yifei, Rathinavelan, Thenmalarchelvi, Roe, Daniel R., Roux, Benoit, Rowley, Christopher N., Shen, Jana, Simmonett, Andrew C., Sodt, Alexander J., Töpfer, Kai, Upadhyay, Meenu, van der Vaart, Arjan, Vazquez-Salazar, Luis Itza, Venable, Richard M., Warrensford, Luke C., Woodcock, H. Lee, Wu, Yujin, Brooks, Charles L., Brooks, Bernard R., Karplus, Martin
Publikováno v:
The Journal of Physical Chemistry - Part B; October 2024, Vol. 128 Issue: 41 p9976-10042, 67p