Molecular dynamics simulations in drug discovery and pharmaceutical development
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …
development process. In this review, we give a broad overview of the current application …
Protein structure-based drug design: from docking to molecular dynamics
P Śledź, A Caflisch - Current opinion in structural biology, 2018 - Elsevier
Highlights•High-throughput docking of small molecules is very successful in hit identification,
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
The all-atom additive CHARMM36 protein force field is widely used in molecular modeling
and simulations. We present its refinement, CHARMM36m (http://mackerell. umaryland …
and simulations. We present its refinement, CHARMM36m (http://mackerell. umaryland …
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 …
N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2
SARS-CoV-2 has been spreading around the world for the past year. Recently, several
variants such as B. 1.1. 7 (alpha), B. 1.351 (beta), and P. 1 (gamma), which share a key …
variants such as B. 1.1. 7 (alpha), B. 1.351 (beta), and P. 1 (gamma), which share a key …
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
Proper treatment of nonbonded interactions is essential for the accuracy of molecular
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …
dynamics (MD) simulations, especially in studies of lipid mono-and bilayers. The use of the …
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
P Eastman, J Swails, JD Chodera… - PLoS computational …, 2017 - journals.plos.org
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It
allows users to easily add new features, including forces with novel functional forms, new …
allows users to easily add new features, including forces with novel functional forms, new …
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 …
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 …