Kallyope
Deciphering the gut-brain axis through AI-driven drug discovery for transformative therapeutics.

The industry-standard R framework for structural bioinformatics and biomolecular dynamics analysis.
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.
Calculates normal modes for large sets of structures simultaneously to identify conserved vibration patterns.
Deciphering the gut-brain axis through AI-driven drug discovery for transformative therapeutics.
Accelerating drug discovery through an end-to-end generative AI pipeline for target identification, molecular design, and clinical trial prediction.
The industry-standard interactive visualization tool for integrated exploration of large-scale genomic datasets.
Unlocking the causal biology of disease through Gemini Digital Twins.
Verified feedback from the global deployment network.
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Quantifies the correlation of atomic fluctuations to reveal long-range allosteric communication within proteins.
Direct wrapper functions to call sequence search and alignment tools within the structural analysis workflow.
Enables exploration of protein conformational space through simplified geometric constraint satisfaction.
Reduces the dimensionality of MD simulation data to visualize major conformational shifts on a 2D or 3D plot.
A sophisticated syntax for selecting subsets of atoms based on name, residue type, or spatial properties.
Maps structural divergence across phylogenetic trees to correlate evolutionary pressure with physical stability.
Identifying non-active site pockets for drug binding in GPCRs.
Registry Updated:2/7/2026
Filter for druggable cavities.
Verifying that an MD simulation has reached equilibrium.
Predicting how a single point mutation affects global protein stability.