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The Amber biomolecular simulation programs
TLDR
The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. Expand
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
TLDR
MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics or Monte Carlo simulations, including the Poisson-Boltzmann Model and several implicit solvation models. Expand
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.
TLDR
This study investigates the capability of the molecular mechanics-generalized Born surface area (GBSA) approach to estimate absolute binding free energies for the protein-protein complexes and finds hotspot residues experience a significantly larger-than-average decrease in local fluctuations upon complex formation. Expand
Knowledge-based scoring function to predict protein-ligand interactions.
TLDR
The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented and is superior to the "chemical scoring" implemented into this tool, while comparable results are obtained using the "energy scoring" in DOCK. Expand
Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf
TLDR
absolute binding free energies are reported for the complex H‐Ras/C‐Raf1 using the MM‐PB(GB)SA approach, testing the internal consistency and model dependence of the results, and the need to exercise caution in applying the computationally cheaper “one‐trajectory‐alternative” to systems where there may be significant changes in flexibility and structure due to binding. Expand
Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method
TLDR
The Molecular Mechanics Poisson–Boltzmann Surface Area approach is an efficient method for the calculation of free energies of diverse molecular systems and has great potential that allows comparative free energy analyses for various molecular systems at low computational cost. Expand
DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction.
TLDR
A necessary prerequisite to successfully resolving the scoring problem with a more discriminative scoring function is the generation of highly accurate ligand poses, which approximate the native pose to below 1 angstroms rmsd, in a docking run. Expand
A toolkit and benchmark study for FRET-restrained high-precision structural modeling
TLDR
A dramatic improvement in the precision of FRET-derived structures is achieved by explicitly considering spatial distributions of dye positions, which greatly reduces uncertainties due to flexible dye linkers. Expand
Histone deacetylase (HDAC) inhibitors with a novel connecting unit linker region reveal a selectivity profile for HDAC4 and HDAC5 with improved activity against chemoresistant cancer cells.
TLDR
Compound 19i (LMK235) (N-((6-(hydroxyamino)-6-oxohexyl)oxy)-3,5-dimethylbenzamide) showed similar effects compared to vorinostat on inhibition of cellular HDACs in a pan-HDAC assay but enhanced cytotoxic effects against the human cancer cell lines A2780, Cal27, Kyse510, and MDA-MB231. Expand
Assessing scoring functions for protein-ligand interactions.
TLDR
Improved modeling of the protonation states leads to a better prediction of binding affinities in the case of the generalized Born and the Poisson continuum models used in conjunction with the CHARMm force field. Expand
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