Developed by the Amaro Lab and designed to be run on Linux, SEEKR is a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory.
The AMBER GPU MD workflow tool aims to increase the reproducibility and scalability of GPU-based AMBER molecular dynamics simulations, by providing an intuitive and comprehensive job management and execution system. The tool assists users in the set-up and execution of publication-quality MD research, including multi-stage minimization, heating, constrained equilibration and multi-copy production dynamics. The tool runs on local GPU(s) and GPU clusters, and the tutorial introduces users to both platforms.
A dataset for Poisson-Boltzmann calculations on biomolecule-ligand systems. This is a subset of the data presented in the book "Computational Electrostatics for Biological Applications (Eds. W. Rocchia & M. Spagnuolo)". The dataset contains structure files in various required formats, input files for PBSA, APBS, and DelPhi.
A plugin for VMD that interfaces with the electrostatics solver DelPhi to provide single frame or ensemble-averaged electrostatic calculations using the Poisson-Boltzmann equation. Allows extensive customization of Delphi input parameters and many other features.
To merely consider a single, frozen structure of a protein, important information may be neglected. Proteins constantly move, change shape, and mutate. FTProd allows a researcher to consider this fluctuations in the analysis and prediction of ligand-binding hot spots.
Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. Weighted Implementation of Suboptimal Paths (WISP) is capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals.