Zobrazeno 1 - 10
of 595
pro vyhledávání: '"Vijay S, Pande"'
Publikováno v:
PLoS Computational Biology, Vol 16, Iss 3, p e1007530 (2020)
This work reports a dynamical Markov state model of CLC-2 "fast" (pore) gating, based on 600 microseconds of molecular dynamics (MD) simulation. In the starting conformation of our CLC-2 model, both outer and inner channel gates are closed. The first
Externí odkaz:
https://doaj.org/article/08fcf7558bfb4ff5b38844dd1262fdfc
Autor:
Evan N. Feinberg, Debnil Sur, Zhenqin Wu, Brooke E. Husic, Huanghao Mai, Yang Li, Saisai Sun, Jianyi Yang, Bharath Ramsundar, Vijay S. Pande
Publikováno v:
ACS Central Science, Vol 4, Iss 11, Pp 1520-1530 (2018)
Externí odkaz:
https://doaj.org/article/d9ff7e5b3ecd43a4b7301d611325923a
Autor:
Hao Yang, Daryl Staveness, Steven M. Ryckbosch, Alison D. Axtman, Brian A. Loy, Alexander B. Barnes, Vijay S. Pande, Jacob Schaefer, Paul A. Wender, Lynette Cegelski
Publikováno v:
ACS Central Science, Vol 4, Iss 1, Pp 89-96 (2018)
Bryostatin 1 (henceforth bryostatin) is in clinical trials for the treatment of Alzheimer’s disease and for HIV/AIDS eradication. It is also a preclinical lead for cancer immunotherapy and other therapeutic indications. Yet nothing is known about t
Externí odkaz:
https://doaj.org/article/0c4021d3b7b3445188b8df92455c1628
Autor:
Matthew P. Harrigan, Keri A. McKiernan, Veerabahu Shanmugasundaram, Rajiah Aldrin Denny, Vijay S. Pande
Publikováno v:
Scientific Reports, Vol 7, Iss 1, Pp 1-8 (2017)
Abstract Two-pore domain potassium (K2P) channel ion conductance is regulated by diverse stimuli that directly or indirectly gate the channel selectivity filter (SF). Recent crystal structures for the TREK-2 member of the K2P family reveal distinct
Externí odkaz:
https://doaj.org/article/dd1ffd3260654a00bc7579dd22c01274
Publikováno v:
Nature Communications, Vol 8, Iss 1, Pp 1-10 (2017)
Natural supplies of bryostatin, a compound in clinical trials for Alzheimer’s disease, cancer, and HIV, are scarce. Here, the authors perform molecular dynamics simulations to understand how bryostatin interacts with membrane-bound protein kinase C
Externí odkaz:
https://doaj.org/article/78cf93730c7546aa81864384d812eaa5
Publikováno v:
Biophysical Journal.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::562643c41b23d31cc1a749a72f3c67cc
https://doi.org/10.1016/j.bpj.2023.03.028
https://doi.org/10.1016/j.bpj.2023.03.028
Publikováno v:
Nature Communications, Vol 7, Iss 1, Pp 1-11 (2016)
Calmodulin is an important calcium sensor that can recognise and interact with a large range of proteins. Here, the authors use molecular dynamics simulations and Markov state models to show that the range of binding conformations adopted without sub
Externí odkaz:
https://doaj.org/article/9e79a6d3f3e04b1184f9366e42aca192
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 6, p e1006176 (2018)
We use reinforcement learning to train an agent for computational RNA design: given a target secondary structure, design a sequence that folds to that structure in silico. Our agent uses a novel graph convolutional architecture allowing a single mode
Externí odkaz:
https://doaj.org/article/84ca18a973b94f29a0e16f8dafe0cbdc
Autor:
Trung Hai Nguyen, Ariën S Rustenburg, Stefan G Krimmer, Hexi Zhang, John D Clark, Paul A Novick, Kim Branson, Vijay S Pande, John D Chodera, David D L Minh
Publikováno v:
PLoS ONE, Vol 13, Iss 9, p e0203224 (2018)
Isothermal titration calorimetry (ITC) is the only technique able to determine both the enthalpy and entropy of noncovalent association in a single experiment. The standard data analysis method based on nonlinear regression, however, provides unreali
Externí odkaz:
https://doaj.org/article/18f5005ec38b4fdb9b413060fb12dc72
Autor:
Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao, Kyle A Beauchamp, Lee-Ping Wang, Andrew C Simmonett, Matthew P Harrigan, Chaya D Stern, Rafal P Wiewiora, Bernard R Brooks, Vijay S Pande
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 7, p e1005659 (2017)
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features
Externí odkaz:
https://doaj.org/article/a3c536fb0ab14c8bbc0cb33e5bac84f0