193 citations · 428 across the 15 of their papers we have counts for
15 papers
Differentiable Rotamer Sampling with Molecular Force Fields
Congzhou M. Sha, Jian Wang, Nikolay V. Dokholyan
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as…
Simple exponential acceleration of the power iteration algorithm
Congzhou M Sha, Nikolay V Dokholyan
Many real-world problems rely on finding eigenvalues and eigenvectors of a matrix. The power iteration algorithm is a simple method for determining the largest eigenvalue and assoc…
Drug Discovery Approaches using Quantum Machine Learning
Junde Li, Mahabubul Alam, Congzhou M Sha +3
Traditional drug discovery pipeline takes several years and cost billions of dollars. Deep generative and predictive models are widely adopted to assist in drug development. Classi…
The architecture of the protein domain universe
Nikolay V. Dokholyan
Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been…
Folding Trp-cage to NMR resolution native structure using a coarse-grained model
Feng Ding, Sergey V. Buldyrev, Nikolay V. Dokholyan
We develop a coarse-grained protein model with a simplified amino acid interaction potential. We perform discrete molecular dynamics folding simulations of a small 20 residue prote…
Molecular Dynamics Simulation of Amyloid Beta Dimer Formation
B. Urbanc, L. Cruz, F. Ding +5
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of…