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MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
TLDR
MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo simulations. Expand
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ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc05720a Click here for
TLDR
We demonstrate how a deep neural network (NN) trained on a data set of quantum mechanical (QM) DFT calculated energies can learn an accurate and transferable atomistic potential for organic molecules containing H, C, N, and O atoms. Expand
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All-atom structure prediction and folding simulations of a stable protein.
We present results from all-atom, fully unrestrained ab initio folding simulations for a stable protein with nontrivial secondary structure elements and a hydrophobic core. The construct, "trpcage",Expand
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Smaller and Faster: The 20-Residue Trp-Cage Protein Folds in 4 μs
We have used laser temperature jump spectroscopy to measure the folding speed of the 20-residue Trp-cage, the smallest polypeptide known to exhibit truly cooperative folding behavior. The observedExpand
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MOIL: A program for simulations of macromolecules
TLDR
A package of computer programs for molecular dynamics simulations-MOIL- is described. Expand
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Molecular and functional characterization of a juvenile hormone acid methyltransferase expressed in the corpora allata of mosquitoes.
A juvenile hormone acid methyltransferase (JHAMT) was isolated as an abundant EST in a library of the corpora allata of the adult female mosquito Aedes aegypti. Its full length cDNA encodes a 278-aaExpand
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Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning.
Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a potentially useful tool for accelerating molecular dynamics (MD) simulations. By repartitioning the mass ofExpand
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Coupling of replica exchange simulations to a non-Boltzmann structure reservoir.
Computing converged ensemble properties remains challenging for large biomolecules. Replica exchange molecular dynamics (REMD) can significantly increase the efficiency of conformational sampling byExpand
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Theoretical study of the isomerization mechanism of azobenzene and disubstituted azobenzene derivatives.
A series of azobenzenes was studied using ab initio methods to determine the substituent effects on the isomerization pathways. Energy barriers were determined from three-dimensional potential energyExpand
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Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics.
We evaluate the efficiency of the pH replica exchange molecular dynamics (pH-REMD) method proposed by Itoh et al. (Proteins2011, 79, 3420-3436) by using it to predict the pKa values of the titratableExpand
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