VMD: Visual molecular dynamics

William Humphrey, Andrew Dalke, Klaus Schulten

Journal of Molecular Graphics

EngineeringVisual Molecular DynamicsMolecular BiologyComputational ChemistryMolecular Dynamics +3

The Protein Data Bank

Helen M. Berman

Nucleic Acids Research

Biological DatabaseBiochemistryStructural BioinformaticsNatural SciencesMedicine +10

Development and testing of a general amber force field

Junmei Wang, Romain M. Wolf, James W. Caldwell, +2

Journal of Computational Chemistry

Crystal StructureEngineeringAmber Force FieldsComputational ChemistryChemistry +16

The PyMOL Molecular Graphics System

Warren L. DeLano

Medical Entomology and Zoology

EngineeringMolecular BiologyMolecular GraphicMolecular RecognitionMedicine +3

Scalable molecular dynamics with NAMD

J. C. Phillips, Rosemary Braun, Wei Wang, +7

Journal of Computational Chemistry

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

Berk Hess, Carsten Kutzner, David van der Spoel, +1

Journal of Chemical Theory and Computation

Cluster ComputingEngineeringMolecular BiologyComputational ChemistryScalable Molecular Simulation +19

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

William L. Jorgensen, David S. Maxwell, Julian Tirado‐Rives

Journal of the American Chemical Society

Organic MoleculesEngineeringConformational EnergeticsPhysicsGas Phase +11

CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields

Kenno Vanommeslaeghe, Elizabeth Hatcher, Chitrangada Acharya, +8

Journal of Computational Chemistry

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Viktor Horn̆ák, Robert Abel, Asim Okur, +3

Proteins Structure Function and Bioinformatics

Automatic atom type and bond type perception in molecular mechanical calculations

Junmei Wang, Wei Wang, Peter A. Kollman, +1

Journal of Molecular Graphics and Modelling

Bond Type PerceptionAutomatic Atom TypeMolecular Mechanical CalculationsEngineeringPhysics +11