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Found 7 papers, 5 papers with code
Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems.
A novel hotspot of gelsolin instability and aggregation propensity triggers a new mechanism of amyloidosis
The multidomain protein gelsolin (GSN) is composed of six homologous modules, sequentially named G1 to G6.
Computational and Experimental Characterization of NF023, A Candidate Anticancer Compound Inhibiting cIAP2/TRAF2 Assembly
Protein-protein interactions are the basis of many important physiological processes and are currently promising, yet difficult, targets for drug discovery.
TorchMD: A deep learning framework for molecular simulations
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials.
How to Differentiate Collective Variables in Free Energy Codes: Computer-Algebra Code Generation and Automatic Differentiation
The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations.
Computational Physics
PLUMED-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment.
Computational Physics Biological Physics Biomolecules
Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules.
Computational Physics Biological Physics Biomolecules
