BIOINFORMATICS TOOLS
Protein Structure Analysis Tools
Protein Structure Modeling
- Swiss Model – Fully automated protein structure homology-modelling server.
- Phyre2 – Protein Homology/analogY Recognition Engine V 2.0.
- SwisDock – A web service to predict the molecular interactions that may occur between a target protein and a small molecule.
- AutoDock – AutoDock is a suite of automated docking tools.
- CASP – Protein structure prediction center.
- Rosetta – The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. Further, it offers de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
Protein 3D Visualization
- Chimera – a program for the interactive visualization and analysis of molecular structures and related data.
- ChimeraX – It is the next-generation interactive molecular visualization program.
- Swiss-PDB Viewer – Application for analyzing several proteins at the same time as well as protein modeling server.
- PyMol – PyMOL is a molecular visualization system maintained and distributed by Schrödinger.
- VMD – Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
- RasMol – Molecular visualization tool.
Must Read
MHub.ai: Standardizing AI for Reproducible Medical Imaging
An inter-institutional collaboration across the US, Germany, and the Netherlands introduces MHub.ai, an accessibility and reproducibility-prioritizing, open source platform for standardized access to AI...
ConGLUDe: Toward General-Purpose Foundation Models for Drug Discovery
Researchers from Johannes Kepler University Linz, Austria, and Merck HealthCare, Germany, developed ConGLUDe (Contrastive Geometric Learning for Unified Computational Drug Design), an AI-based model for drug...
Claude Opus 4.5 and the Future of AI-Driven Research in Healthcare and Biotechnology
The growing complexity of biomedical research and healthcare demands AI systems that can go beyond general assistance to support end-to-end scientific workflows. Building on...
DrugCLIP Enables High-Throughput Virtual Screening Across the Human Proteome
Researchers at Tsinghua University have introduced DrugCLIP, a contrastive learning framework that enables ultrafast and accurate virtual screening at a genome-wide scale. Published in...
Beyond the Sequence: How FoldMason is Redefining Multiple Protein Structure Alignment at Scale
The authors at Seoul National University developed FoldMason, a free, open-source, progressive Multiple Structural Alignment (MSTA) method published in Science that uses a structural...