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HotSpot Wizard
A web app to identifye automatically hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. HotSpot Wizard integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. The method provides comprehensive annotations of protein structures and assists protein engineers with the rational design of site-specific mutations and focused libraries.favourite protein and for the design of mutations in site-directed mutagenesis and focused directed evolution experiments.
KFC Server / Knowledge-based FADE and Contacts Server
Allows users to detect binding hot spots in protein-protein interfaces. KFC Server is web application that investigates chemical and physical features into a macromolecular structure to point it out characteristics signaling important binding contacts. The interface provides an optional functionality that permits to run the original algorithm. Besides, it also includes a job viewer including a molecular viewer coupled to a control panel.
HotPoint
Allows to determine computational hot spots in protein interfaces. HotPoint is a web server based on solvent accessibility and pair potentials which allows online calculation for all protein interfaces within practical running times. The software tabulates residue level features and prediction results for a given protein complex which are also downloadable. It can be useful both for the experimentalists and computational scientist working on protein recognition, modeling of protein complexes and drug design.
PocketQuery
A web interface for exploring the properties of protein-protein interaction (PPI) interfaces with a focus on the discovery of promising starting points for small-molecule design. PocketQuery rapidly focuses attention on the key interacting residues of an interaction using a 'druggability' score that provides an estimate of how likely the chemical mimicry of a cluster of interface residues would result in a small-molecule inhibitor of an interaction. PocketQuery provides an easy to use graphical interface for searching for clusters, displaying and browsing the clusters that are the results of a search, and visualizing the molecular structure and properties of clusters within the 3D PPI structure.
Peptiderive
A web server which is incorporated within the ROSIE web interface for Rosetta protocols. Peptiderive protocol identifies, in a given structure of a protein-protein interaction, the linear polypeptide segment suggested to contribute most to binding energy. Interactions that feature a ‘hot segment’, a linear peptide with significant binding energy compared to that of the complex, may be amenable for inhibition and the peptide sequence and structure derived from the interaction provide a starting point for rational drug design.
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