CHARMM: the biomolecular simulation program
Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …
widely used molecular simulation program. It has been developed over the last three …
Jaguar: A high‐performance quantum chemistry software program with strengths in life and materials sciences
Jaguar is an ab initio quantum chemical program that specializes in fast electronic structure
predictions for molecular systems of medium and large size. Jaguar focuses on …
predictions for molecular systems of medium and large size. Jaguar focuses on …
SWISS-MODEL: homology modelling of protein structures and complexes
A Waterhouse, M Bertoni, S Bienert… - Nucleic acids …, 2018 - academic.oup.com
Homology modelling has matured into an important technique in structural biology,
significantly contributing to narrowing the gap between known protein sequences and …
significantly contributing to narrowing the gap between known protein sequences and …
ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB
JA Maier, C Martinez, K Kasavajhala… - Journal of chemical …, 2015 - ACS Publications
Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force
field is required. The Amber ff99SB force field improved protein secondary structure balance …
field is required. The Amber ff99SB force field improved protein secondary structure balance …
ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution
Molecular dynamics (MD) simulations have become increasingly popular in studying the
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
OPLS3: a force field providing broad coverage of drug-like small molecules and proteins
The parametrization and validation of the OPLS3 force field for small molecules and proteins
are reported. Enhancements with respect to the previous version (OPLS2. 1) include the …
are reported. Enhancements with respect to the previous version (OPLS2. 1) include the …
Improvements to the APBS biomolecular solvation software suite
Abstract The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages that have …
the equations of continuum electrostatics for large biomolecular assemblages that have …
CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data
Protein structure and dynamics can be characterized on the atomistic level with both nuclear
magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here …
magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here …
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
While the quality of the current CHARMM22/CMAP additive force field for proteins has been
demonstrated in a large number of applications, limitations in the model with respect to the …
demonstrated in a large number of applications, limitations in the model with respect to the …
PLUMED 2: New feathers for an old bird
Enhancing sampling and analyzing simulations are central issues in molecular simulation.
Recently, we introduced PLUMED, an open-source plug-in that provides some of the most …
Recently, we introduced PLUMED, an open-source plug-in that provides some of the most …