Structural Biology

WHISCY is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein.

GOblet is a comprehensive web server application providing the annotation of anonymous sequence data with Gene Ontology (GO) terms. It uses a variety of different protein databases (human, murines, invertebrates, plants, sp-trembl) and their respective GO mappings. The user selects the appropriate database and alignment threshold and thereafter submits single or multiple nucleotide or protein sequences.

CheckHBond evaluates whether a hydrogen bond can be formed between two residues in a PDB structure, allowing you to specify the amino acid present at the second position.

MatrixPlot can be used to generate mutual information plots of sequence alignments, distance matrices of sequence with known 3D coordinates, and plots of user provided matrix files.

FeatureMap3D combines protein sequence-based information with structural data from the Protein Data Bank (PDB).Each query sequence is aligned to the best hit in PDB. The hit is visualized by mapping the alignment onto the PDB structure using color-coding for match/mismatch gaps etc.

Automatic molecular modeling of proteins 3D structure.

3D-JIGSAW builds three-dimensional models for proteins based on homologues of known structure.

A tool in the understanding of limited proteolysis.The program works by calculating a series of prediction parameters for a given protein structure and then processing them to produce a final prediction score for each amino acid residue in a protein chain. This is achieved by averaging parameter scores for each residue position over a moving window. Hence, likely sites of limited proteolysis on a known protein structure from the Brookhaven databank can be assigned on this basis.

Crescendo is a program for identifying functional sites in proteins. It distinguishes structural and functional restraints in evolution in order to identify interaction sites.

EmpiricaL Enhancement of Predicted HelicAl N-Termini.The algorithm has been designed to work primarily on secondary structures predicted by JPred or PHD.