Targeting cryptic-orthosteric site of PD-L1 for inhibitor identification using structure-guided approach

VMD: Visual molecular dynamics

William Humphrey, Andrew Dalke, Klaus Schulten · Journal of Molecular Graphics · 1996 · 64.1K citations

Engineering, Visual Molecular Dynamics, Molecular Biology +5

Development and testing of a general amber force field

Junmei Wang, Romain M. Wolf, James W. Caldwell et al. · Journal of Computational Chemistry · 2004 · 18.8K citations

Crystal Structure, Engineering, Amber Force Fields +18

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James Maier, Carmenza Martinez, Koushik Kasavajhala et al. · Journal of Chemical Theory and Computation · 2015 · 10.6K citations · Full text

Structural Bioinformatics, Biomolecular Structure Prediction, Amber Ff12sb Parameter +24

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe, Thomas E. Cheatham · Journal of Chemical Theory and Computation · 2013 · 7.3K citations

Engineering, Molecular Biology, Amber Package +16

Extra Precision Glide:  Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

Richard A. Friesner, Robert B. Murphy, Matthew P. Repasky et al. · Journal of Medicinal Chemistry · 2006 · 6.7K citations