| Structure Databases | Structure/Sequence Manipulation Software | Modeling/Predicting |
|---|---|---|
| Protein Databank | Rasmol (Selection and Scripting) |
Build a Protein |
| Enzyme Structures and Classification |
WebLab Viewer Lite (Alter Structures) |
Predict Protein Server (Secondary Structure) |
| Peptidases | Swiss PDB Viewer (Structure Alignment, Mutation, Homology Modeling) |
PsiPred Server (Secondary Structure) |
| HIV Database | Kinemage (The Original) |
NNPredict (Secondary Structure) |
| PDBSum | Geneious Many tools, including PubMed search |
Modeller (Homology Modeling) |
| Entrez Structure | PyMol (Ray-traced graphics) |
SwissModel (Homology Modeling) |
| Expasy (the Swiss Institute of Bioinformatics) | VMD (Display MD simulations) |
DisEMBL Server (Predict Disordered Regions) |
| Atlas of Enzyme Catalytic Sites | Python Molecule Viewer (part of MGL Tools) |
Rosetta Server (Complete 3-D Structure) |
| Protein Informatics Resource | MolSoft Browser | Predict Protein secondary and Tertiary Structure |
| ProDom Database of Evolutionary Domains |
UCSF Chimera Graphics, numerous modeling tools |
3D-Fun Predict Function from Structure |
| PDBSum (analysis of protein structure) | JalView (sequence alignment) | ProFunc Server (Predict protein function from structure) |
| NCBI - Entrez (GeneBank, etc.) |
Jmol Structure Viewer | ProSite Server (Predict protein function from sequence) |
| CAPRI - Critical Assessment of Predicted Interactions |
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| FREE Programs for Drawing Organic Chemistry Style Line Structures (PC) | ||
| WinDrawChem | WinPlot | ChemSketch |
| FREE Programs for Drawing Organic Chemistry Style Line Structures (Mac)) | ||
| IsisDraw | Marvin Sketch (Java) | |
Rasmol is the easiest to use stand-alone viewer; PyMol is more complex, but makes better pictures. You MUST have access to a computer onto which you can install several programs, like Rasmol. PDB files and Rasmol scripts can be edited with any ASCII text editor. Here is a link to a good FREE one, called PFE.