Abstract
We present extensive updates to Bio3D, a package for both interactive and batch analysis of biomolecular structure, sequence and molecular simulation data. These updates include unique high-throughput ensemble normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, new consensus methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis, interactive structure ensemble visualization as well as multicore support for many time intensive tasks. We demonstrate a new online WebApp server powered by Bio3D for comparative protein structure analysis. This server facilitates: (1) The identification of related protein structures to user specified thresholds of similarity; (2) Their alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) ensemble normal mode analysis for comparison of predicted deformations across protein families. The WebApp offer unparalleled capabilities for ensemble analysis of protein structures in a user friendly web browser environment from http://thegrantlab.org/bio3d/webapps. The previous version of Bio3D has been downloaded by over 13,700 researchers and cited over 200 times in the last six years. Merging these new methods with the existing Bio3D infrastructure 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 and associated WebApps are distributed with full source code and extensive documentation under a GPL2 license from http://thegrantlab.org/bio3d/.
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