Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics

Autor: David L. Mobley, Sukanya Sasmal, Samuel C. Gill, Nathan M. Lim

Publikováno v: J Chem Theory Comput
Journal of chemical theory and computation, vol 16, iss 3

Flexible ligands often have multiple binding modes or bound conformations that differ by rotation of a portion of the molecule around internal rotatable bonds. Knowledge of these binding modes is important for understanding the interactions stabilizi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a94cbf828702dffa4ecb91332318e5cf
https://doi.org/10.1021/acs.jctc.9b01066

Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins

Autor: Sukanya Sasmal, Sara Y. Cheng, Julie D. Forman-Kay, Teresa Head-Gordon, Robert M. Vernon, Akshaya K. Das, Meili Liu, James Lincoff

Publikováno v: International journal of molecular sciences, vol 22, iss 7
International Journal of Molecular Sciences
Volume 22
Issue 7
International Journal of Molecular Sciences, Vol 22, Iss 3420, p 3420 (2021)

Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve the description of IDPs/IDRs but are largely in disagreement with solution experime

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d811679e7b45df2eccad6e6ac3571d42
https://escholarship.org/uc/item/79t1536z

Comparison of Ligand Affinity Ranking Using AutoDock-GPU and MM-GBSA Scores in the D3R Grand Challenge 4

Autor: Giulia Bianco, Jerome Eberhardt, David L. Mobley, Léa El Khoury, Diogo Santos-Martins, Francesca Alessandra Ambrosio, Stefano Forli, Andreas Koch, Leonardo Solis-Vasquez, Sukanya Sasmal

Molecular docking has been successfully used in computer-aided molecular design projects for the identification of ligand poses within protein binding sites. However, relying on docking scores to rank different ligands with respect to their experimen

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::111b040b266129194a5329976e3da024
https://doi.org/10.26434/chemrxiv.8309690

Effect of a Paramagnetic Spin Label on the Intrinsically Disordered Peptide Ensemble of Amyloid-β

Autor: Teresa Head-Gordon, Sukanya Sasmal, James Lincoff

Publikováno v: Biophysical journal, vol 113, iss 5
Sasmal, S; Lincoff, J; & Head-Gordon, T. (2017). Effect of a Paramagnetic Spin Label on the Intrinsically Disordered Peptide Ensemble of Amyloid-β. Biophysical Journal, 113(5), 1002-1011. doi: 10.1016/j.bpj.2017.06.067. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/559052kd

© 2017 Biophysical Society Paramagnetic relaxation enhancement is an NMR technique that has yielded important insight into the structure of folded proteins, although the perturbation introduced by the large spin probe might be thought to diminish it

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ba52b96dbe142642fcff2278579492c6
https://pubmed.ncbi.nlm.nih.gov/28877484

Mechanism of nucleation and growth of Aβ40 fibrils from all-atom and coarse-grained simulations

Autor: Teresa Head-Gordon, Sukanya Sasmal, Nadine Schwierz

Publikováno v: Sasmal, S; Schwierz, N; & Head-Gordon, T. (2016). Mechanism of nucleation and growth of Aβ40 fibrils from all-atom and coarse-grained simulations. Journal of Physical Chemistry B, 120(47), 12088-12097. doi: 10.1021/acs.jpcb.6b09655. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/5x20x3z4
The journal of physical chemistry. B, vol 120, iss 47

© 2016 American Chemical Society. In this work, we characterize the nucleation and elongation mechanisms of the "diseased" polymorph of the amyloid-β 40 (Aβ40) fibril using an off-lattice coarse-grained (CG) protein model. After determining the nu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3c2191ef1062a0ff478724b7dbd3c52d
http://www.escholarship.org/uc/item/5x20x3z4