2 citations · 5 across the 6 of their papers we have counts for
6 papers
Extending fragment-based free energy calculations with library Monte Carlo simulation: Annealing in interaction space
Steven Lettieri, Artem B. Mamonov, Daniel M. Zuckerman
Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via "library-based Monte Carlo") and for obtaining…
Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Studied Using Well-Sampled Semi-Atomistic Simulations
Derek J. Cashman, Artem B. Mamonov, Divesh Bhatt +1
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. In this computational study, we studied the prot…
Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo
Ying Ding, Artem B. Mamonov, Daniel M. Zuckerman
We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling…
Rapid sampling of all-atom peptides using a library-based polymer-growth approach
A. B. Mamonov, X. Zhang, D. M. Zuckerman
We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with implicit solvent. The main novel feature of our ap…
Absolute free energies estimated by combining pre-calculated molecular fragment libraries
Xin Zhang, Artem B. Mamonov, Daniel M. Zuckerman
The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practica…
A library-based Monte Carlo technique enables rapid equilibrium sampling of a protein model with atomistic components
Artem B. Mamonov, Divesh Bhatt, Derek J. Cashman +1
There is significant interest in rapid protein simulations because of the time-scale limitations of all-atom methods. Exploiting the low cost and great availability of computer mem…