Structure prediction links:

BioInfoBank Institute
COILS - Prediction of Coiled Coil Regions in Proteins
REPRO - Protein Repeats Analysis
DSSP - a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB)
FFAS03 - Fold & Function Assignment System
Pfam - a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.
HMMER - profile HMMs for protein sequence analysis
JUFO - This server offers a protein secondary structure prediction from its primary sequence only. An neural network was trained with an amino acid property profile and the position based scoring matrix of a blast run.
JUFO3D
Protein-Protein BLAST - At the NCBI.
MAMMOTH - MAtching Molecular Models Obtained from THeory
Data formats for Robetta
BLAST - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
SAM-T99 - HMM-based Protein Sequence Analysis, SAM-T99
SAM - Sequence Alignment and Modeling System
TMHMM - Prediction of transmembrane helices in proteins
Data formats for Robetta