Resources

AMBER GPU Molecular Dynamics (MD) Workflow Tool and Tutorial

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.

CEBA Dataset - Developed by Jesper Sørensen

A dataset for Possion-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.

DelEnsembleElec - Developed by Lane Votapka and Luke Czapla

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.

FTProd - Developed by Lane Votapka

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.

WISP - Developed by Jacob Durrant, Lane Votapka, and Adam Van Wart

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.