Bio3D

Bio3D is a comprehensive R package specifically designed for the analysis of biomolecular structure, sequence, and trajectory data. As of 2026, Bio3D remains a critical pillar in the structural biology ecosystem, bridging the gap between static protein structure prediction (e.g., AlphaFold3) and functional dynamic analysis. Its architecture leverages the high-performance computing capabilities of R to facilitate the processing of massive ensembles of structures, including those generated by Molecular Dynamics (MD) simulations. Key functionalities include Normal Mode Analysis (NMA) for predicting large-scale protein motions, Principal Component Analysis (PCA) for identifying dominant conformational changes, and extensive utilities for PDB manipulation and sequence-structure mapping. The package is built for interoperability, seamlessly integrating with external tools such as MUSCLE for alignment and VMD/PyMOL for visualization. In the current market, Bio3D is the primary choice for researchers requiring high-throughput, reproducible pipelines for structural evolution studies and drug discovery workflows where conformational flexibility is a decisive factor.