Protein and Assembly Modeling
Servers
Bioinformatics Toolkit (Soding Lab)
I-TASSER (Protein structure prediction)
FUGUE (Threading server)
PSIPRED (secondary structure and fold prediction)
DisProt (Prediction of disordered protein segments
Sequence Alignment
Software
MODELLER (Homology modeling)
Integrative Modeling Platform (Assembly modeling)
Databases
Structural Biology
RCSB PDB (atomic structures)
PDBe (atomic structures)
EMDB (Electron Microscopy densities)
Database of Macromolecular Movements
CATH (protein classifications)
Proteins
UniProt
UCSD Nature Signaling Gateway
Protein-Protein Interactions
The Biogrid (High- and Low throughput interaction data)
iHOP - Information Hyperlinked over Proteins (literature mining)
UCSF Interactome (Krogan and Gavin HT data)
GenRE - CYGD - The Comprehensive Yeast Genome Database
Cryoelectron Microscopy
General
3DEM (3D electron microscopy community homepage)
European Microscopy Society
Image Processing Software
TOM doc
SPIDER doc (Wadsworth)
EMAN2 / SPARX
XMIPP doc
Visualization
PyMol Wiki
UCSF Chimera Volume display
UCSF Chimera Users Guide
Data acquisition using SerialEM
SerialEM Macros
Direct Detector Functions
Useful Macros from Brandeis
