Given a set of protein sequences (in fasta format), InterPreTS will use BLAST to find homologues of known structure for all pairs (i.e. templates that can model each pair of sequences based on homology) and then evaluate the suitability of those templates for modelling the interaction
ProTSAV is a meta-server, which has a collection of model quality assessment programs that evaluate the quality of a protein and correctness of the structural model.
The PEPstrMOD server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. It also handles peptides having various modifications like non-natural residues, terminal modifications (Acetylation/Amidation), Cyclization (N-C, disulfide bridges), conversion of L- to D- amino acids, post translational modifications, etc. The prediction strategy is based on the realization that β-turn is an important and consistent feature of small peptides in addition to regular structures. Thus, the method uses both the regular secondary structure information predicted from PSIPRED and β-turns information predicted from BetaTurns. The structure is further refined with energy minimization and molecular dynamic simulations.