Codes and Resources
T-Analyst: a program for efficient analysis of protein conformational changes
T-Analyst is a program for analyzing molecular dynamics trajectories based on internal bond-angle-torsion coordinates. The program computes entropy and rotameric states of dihedrals, clusters multiple conformations and detects dihedral rotations that contribute hinge-like motions. T-Analyst was developed with special focuses on showing changes of protein flexibility between different states, and selecting representative protein conformations for molecular docking studies.
RedMD (Reduced Molecular Dynamics) developed by Prof. Trylska Lab
RedMD is a an open source software to perform molecular dynamics simulations for coarse-grained models of proteins, nucleic acids and their complexes. Simulations can be carried out in the microcanonical ensemble, with Berendsen and Langevin thermostats, as well as with Brownian dynamics. We provide tools to generate initial conﬁguration and topology from the PDB or PDB XML file formats. Force fields are based on the elastic network approach and its extensions. The code is written in C/C++ languages and the structure/topology of a molecule is based on an XML format. The software is OpenMP parallelized and available for Linux under the GPL license.