Bio3D

Bio3D provides a suite of R packages for analysis of biomolecular sequence, structure, and dynamics to investigate protein sequence-structure-function relationships.

Key Features:

• Suite of R packages: A family of R packages that separate analysis tasks into distinct modules for sequence, structure, and dynamics analyses.
• Biomolecular database searching and retrieval: Functions for searching and retrieving biomolecular data required for comparative and ensemble analyses.
• Sequence and structure conservation analysis: Tools to quantify sequence and structural conservation across homologous proteins.
• Ensemble normal mode analysis: Ensemble normal mode analysis for studying collective motions and protein dynamics.
• Protein structure and correlation network analysis: Methods for protein structure analysis and correlation network analysis to elucidate relationships among structural elements.
• Multivariate analysis (PCA): Multivariate analysis including principal component analysis (PCA) for dimensionality reduction of conformational ensembles.
• Ensemble difference distance matrix analysis (eDDM): eDDM that calculates and compares atomic distance matrices across homologous structures to identify residue-specific determinants of function.
• Bio3D-eddm integration: Bio3D-eddm package capabilities to combine experimental and theoretical simulation-generated structures for joint analysis.
• Automated and reproducible analysis: Support for automated and reproducible dissection of sequence-structure-function relationships.

Scientific Applications:

• Structural biology: Analysis of protein structure, conservation, and dynamics to inform structural biology studies.
• Computational biochemistry: Investigation of conformational dynamics and mechanistic hypotheses in computational biochemistry.
• Residue-specific determinant identification: Identification of residue-specific determinants underlying functional processes using eDDM comparisons.
• Comparative homolog analysis: Comparative analyses across homologous structures using distance matrices and conservation metrics.
• Conformational change characterization: Characterization of large-scale conformational changes and dynamic behaviors using PCA and normal mode analysis.

Methodology:

Methods explicitly include biomolecular database searching and retrieval; sequence and structure conservation analysis; ensemble normal mode analysis; protein structure and correlation network analysis; multivariate analysis including principal component analysis (PCA); ensemble difference distance matrix analysis (eDDM) via calculation and comparison of atomic distance matrices across homologous structures; and integration of experimental and simulation-generated structures through the Bio3D-eddm package.