Proteins are amino acid polymers that are involved in all aspects of cellular function. The structure of a protein is defined by its particular amino acid sequence, with the amino acid sequence being referred to as the primary protein structure. The amino acids fold up in local structural elements; helices and sheets, also called the secondary structure of the protein. These structural elements are then packed into globular folds, known as the tertiary structure or the three dimensional structure.
In order to understand protein function it is often valuable to see the three dimensional structure of the protein. This is possible when the structure of the protein has been resolved and published. Structure files are usually deposited in the Protein Data Bank (PDB) http://www.rcsb.org/, where the publicly available protein structure files can be searched and downloaded. The vast majority of the protein structures have been determined by X-ray crystallography (88%) while the rest of the structures predominantly have been obtained by Nuclear Magnetic Resonance techniques.
In addition to protein structures, the PDB entries also contain structural information about molecules that interact with the protein, such as nucleic acids, ligands, cofactors, and water. There are also entries, which contain nucleic acids and no protein structure. The 3D Molecule Viewer in the Biomedical Genomics Workbench is an integrated viewer of such structure files.
The 3D Molecule Viewer offers a range of tools for inspection and visualization of molecular structures:
- Automatic sorting of molecules into categories: Proteins, Nucleic acids, Ligands, Cofactors, Water molecules
- Hide/unhide individual molecules from the view
- Four different atom-based molecule visualizations
- Backbone visualization for proteins and nucleic acids
- Molecular surface visualization
- Selection of different color schemes for each molecule visualization
- Customized visualization for user selected atoms
- Alignment of protein structures
- Browse amino acids and nucleic acids from sequence editors started from within the 3D Molecule Viewer
- Link a sequence or alignment to a protein structure
- Transfer annotations between the linked sequence and the structure
- Importing molecule structure files
- Viewing molecular structures in 3D
- Customizing the visualization
- Snapshots of the molecule visualization
- Tools for linking sequence and structure
- Protein structure alignment