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
Towards Fully Autonomous Molecular Dynamics: The DynaMate Framework
Researchers from École Polytechnique Fédérale de Lausanne (EPFL) and the National Centre of Competence in Research (NCCR) Catalysis, Switzerland, introduced DynaMate, an autonomous AI system that...
How SPURS Unlocks Scalable and Accurate Protein Stability Prediction
Protein engineering is in the middle of a quiet revolution, and a new study from researchers at the School of Computational Science and Engineering,...
Placing Every Atom Right: PEARL’s Deep Learning Approach to Drug Discovery
Genesis Molecular AI and NVIDIA have introduced PEARL (Placing Every Atom in the Right Location), a deep learning foundation model designed for large-scale protein–ligand cofolding...
Agentic AI Meets RNA‑seq: A New Co‑Pilot For Downstream Analysis
Next-generation sequencing has transformed gene expression profiling into a routine experiment, but interpreting those matrices remains a challenge for many labs. Researchers from Kyungpook...
Teaching Genomics Made Easy: Meet eduomics, the Automated Omics Simulation Pipeline
When researchers at the Department of Biology and Biotechnology, the University of Pavia, set out to rethink bioinformatics teaching. They started from a simple...