DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories
S. V. Gorelov, A. I. Titov, Olga Tolicheva, Andrey L. Konevega, А. В. Швецов
Abstract
This work describes a fast implementation of a software algorithm associated with determination of protein secondary structure based on the Define Secondary Structure of Proteins (DSSP) algorithm. This implementation is fully compatible with the DSSP v.4 and DSSP v.2 algorithms and implemented as a native GROMACS trajectory analysis module, which allows us to analyze molecular dynamics trajectories without any restrictions of the original DSSP implementation. This implementation works much faster than the original DSSP v.4 and DSSP v.2 algorithms.
Topics & Concepts
SoftwareComputer scienceAlgorithmComputational scienceProgramming languageProtein Structure and DynamicsEnzyme Structure and FunctionMass Spectrometry Techniques and Applications