The Bio3D Package: New Interactive Tools for Structural Bioinformatics

Abstract

We present extensive updates to Bio3D, a package for the interactive analysis of biomolecular structure, sequence and molecular simulation data. Features include the ability to read and write biomolecular structure, sequence and dynamic trajectory data, query and search online sequence and structure databases, perform alignment, structural superposition, rigid core and dynamic domain identification, sequence and conformational clustering, distance and correlation matrix analysis, conservation analysis, normal mode analysis, principal component analysis, and many other common structural bioinformatics tasks. Bio3D also leverages the extensive graphical and statistical capabilities of the R environment (http://www.r-project.org) and thus provides a useful framework for the exploratory interactive analysis of biomolecular sequence and structure data. Recent notable additions to the package include consensus dynamical community analysis of network based coupled motions, enhanced coarse grained force fields and methods for normal mode analysis, and multicore support for many time intensive tasks. Here we describe these new capabilities with example applications. The previous version of Bio3D has been downloaded by over 13,700 researchers and cited over 100 times in the last six years. Merging these new methods represents an important advance that we hope will further stimulate biophysicists to use structural bioinformatics methods as an aid in solving their research problems. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/.