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 …
How water's properties are encoded in its molecular structure and energies
How are water's material properties encoded within the structure of the water molecule? This
is pertinent to understanding Earth's living systems, its materials, its geochemistry and …
is pertinent to understanding Earth's living systems, its materials, its geochemistry and …
[HTML][HTML] A guide to in silico drug design
The drug discovery process is a rocky path that is full of challenges, with the result that very
few candidates progress from hit compound to a commercially available product, often due …
few candidates progress from hit compound to a commercially available product, often due …
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
The Molecular Mechanics/Poisson− Boltzmann Surface Area (MM/PBSA) and the Molecular
Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free …
Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free …
SIRT4 is a lysine deacylase that controls leucine metabolism and insulin secretion
Sirtuins are NAD+-dependent protein deacylases that regulate several aspects of
metabolism and aging. In contrast to the other mammalian sirtuins, the primary enzymatic …
metabolism and aging. In contrast to the other mammalian sirtuins, the primary enzymatic …
The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling
A novel energy model (VSGB 2.0) for high resolution protein structure modeling is
described, which features an optimized implicit solvent model as well as physics‐based …
described, which features an optimized implicit solvent model as well as physics‐based …
Identification of post-digestion angiotensin-I converting enzyme (ACE) inhibitory peptides from soybean protein Isolate: Their production conditions and in silico …
Z Xu, C Wu, D Sun-Waterhouse, T Zhao… - Food Chemistry, 2021 - Elsevier
This study attempts to investigate natural angiotensin-I converting enzyme (ACE) inhibitors.
Soybean protein isolated (SPI) hydrolysate (SPIH) was prepared by Alcalase from …
Soybean protein isolated (SPI) hydrolysate (SPIH) was prepared by Alcalase from …
The Amber biomolecular simulation programs
We describe the development, current features, and some directions for future development
of the Amber package of computer programs. This package evolved from a program that was …
of the Amber package of computer programs. This package evolved from a program that was …
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 …
[PDF][PDF] Amber 10
Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …
dynamics simulations, particularly on biomolecules. None of the individual programs carries …