The Protein Data Bank is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids.
We can visualize and analyze structures deposited in this database using a range of software.
Licensed software for 3D structure determination and analysis
Coot
A tool for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.
Coot displays maps and models, and allows model manipulations such as:
- Idealization
- Real space refinement
- Manual rotation/translation
- Rigid-body fitting
- Ligand search
- Solvation
- Mutations
- Rotamers
- Ramachandran plots
- Skeletonization
- Non-crystallographic symmetry and more
PHENIX
A software suite for the automated determination of macromolecular structures using X-ray crystallography methods.
CCP4
A suite of programs covering all aspects of crystallographic structure determination, refinement and analysis.
SHELX
A set of programs for direct structure solution and refinement with high-resolution diffraction data.
HKL2000
A tool for processing X-ray data collected by the Rigaku Saturn 944+ CCD detector.
Licensed software for molecular graphics and structure visualization
PyMOL
A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery. PyMOL is scriptable and can be extended using the Python language. It supports Windows, Mac OSX, Unix, and Linux.
RasMol
A free viewing system for PDB coordinate files that runs on Mac PPC, Windows, Unix, and Linux systems. Open source versions are also available.
Swiss PDB viewer
A 3D graphics and molecular modeling program for the simultaneous analysis of multiple models and for model-building into electron density maps.