End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
Water determines the structure and dynamics of proteins
Water is an essential participant in the stability, structure, dynamics, and function of proteins
and other biomolecules. Thermodynamically, changes in the aqueous environment affect …
and other biomolecules. Thermodynamically, changes in the aqueous environment affect …
OPLS4: Improving force field accuracy on challenging regimes of chemical space
We report on the development and validation of the OPLS4 force field. OPLS4 builds upon
our previous work with OPLS3e to improve model accuracy on challenging regimes of drug …
our previous work with OPLS3e to improve model accuracy on challenging regimes of drug …
[HTML][HTML] A fast and high-quality charge model for the next generation general AMBER force field
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the
world to perform in silico simulations and modelings on diverse scientific topics, especially in …
world to perform in silico simulations and modelings on diverse scientific topics, especially in …
Systematic comparison of the structural and dynamic properties of commonly used water models for molecular dynamics simulations
SP Kadaoluwa Pathirannahalage… - Journal of Chemical …, 2021 - ACS Publications
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions,
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …
1.14* CM1A-LBCC: localized bond-charge corrected CM1A charges for condensed-phase simulations
The quality of the 1.14* CM1A and 1.20* CM5 charge models was evaluated for calculations
of free energies of hydration. For a set of 426 neutral molecules, 1.14* CM1A and 1.20* CM5 …
of free energies of hydration. For a set of 426 neutral molecules, 1.14* CM1A and 1.20* CM5 …
Building water models: a different approach
Simplified classical water models are currently an indispensable component in practical
atomistic simulations. Yet, despite several decades of intense research, these models are …
atomistic simulations. Yet, despite several decades of intense research, these models are …
Guidelines for the analysis of free energy calculations
Free energy calculations based on molecular dynamics simulations show considerable
promise for applications ranging from drug discovery to prediction of physical properties and …
promise for applications ranging from drug discovery to prediction of physical properties and …
An automated force field topology builder (ATB) and repository: version 1.0
The Automated force field Topology Builder (ATB, http://compbio. biosci. uq. edu. au/atb) is a
Web-accessible server that can provide topologies and parameters for a wide range of …
Web-accessible server that can provide topologies and parameters for a wide range of …
FreeSolv: a database of experimental and calculated hydration free energies, with input files
DL Mobley, JP Guthrie - Journal of computer-aided molecular design, 2014 - Springer
This work provides a curated database of experimental and calculated hydration free
energies for small neutral molecules in water, along with molecular structures, input files …
energies for small neutral molecules in water, along with molecular structures, input files …