ProtChemSI ProtChemSI A database of protein-chemical interactions predicted by structure superimpositions: if you are interested in chemicals that might bind a particular protein or vice versa, then check it out.
From Kalinina et al, PLoS Comp Biol, 2011.

pepsite PepSite A method to predict the location of peptide binding sites on protein surfaces: if you have a protein structure and a known or putative peptide that binds to it, pepsite is for you.
From Petsalaki et al, PLoS Comp Biol, 2009.

3DRepertoire 3D Repertoire A European Commission 6th Framework Integrated Project. Our group maintains most of the informatics related to this project.
YeastComplexes Yeast complexes web site data derived from TAP/MS purifications
From Gavin, Aloy et al Nature, 440, 631, 2006
LMD Linear Motif Discovery
From Neduva et al PLoS Biology, 3, e405, 2005
3DID 3D-ID: Interacting domains in three-dimensions From Stein et al Nucl. Acids Res, 33, D413-4178, 2005
3SOM 3SOM: 3D Surface Overlap Maximization
From Ceulemans & Russell J. Mol. Biol., 338, 783-793, 2004
miRNA Drosophila MicroRNA target predictions
From Stark et al PLoS Biology, 1, 397-409, 2003
DisEMBL DisEMBL: Intrinsic Protein Disorder Prediction
From Linding et al, Structure, 11, 1453-1459, 2004
PINTS PINTS: Patterns In Non-homologous Tertiary Structures
Based on Stark et al, J. Mol. Biol., 326, 1307-1316, 2003.
InterPreTS Interaction Prediction through Tertiary Structure
Based on Aloy & Russell, Proc Natl Acad Sci USA, 99 : 5896-5901, 2002.
PROUST2 Prediction Of Unknown Sub-types (PROUST) II
Based on Hannenhalli & Russell, JMB, 303, 61-76, 2000.
COILS Coiled-coil prediction
Based on Lupas et al, Science, 252, 1162-1164, 1991.
AAS Properties of the amino acids
See also Betts & Russell, Amino acid properties and consequences of subsitutions,
Bioinformatics for Geneticists, M.Barnes & Ian Gray eds, Wiley, 2002.