SAINT2 is a fragment-based de novo protein structure prediction software. It is based on the notion that some proteins fold as they are being synthesised, which is known as the cotranslational protein folding hypothesis.
MaxCluster (MaxSub and Clustering) is a command-line tool for the comparison of protein structures. It provides a simple interface for a large number of common structure comparison tasks. A key feature of the program is the ability to process thousands of structures, either against a single reference protein or in an all-verses-all comparison. ::DEVELOPER
SuperMimic is a tool for conformer based fitting of peptide mimetics into protein structures.Many protein recognition mechanisms, mostly involving other proteins or peptides, are known, and more and more of them are being deciphered. To intervent these interactions is the main goal of drug design. As peptides are often poor drug candidates, the need for bioequivalent compounds with better pharmacological properties arises. Starting from a known spatial structure, the goal is to find compounds that mimic the function of a peptide while obtaining improved cellular transport properties, stable structures and resistance against proteases.
The approach used in the program SuperMimic is to identify peptide mimetics starting from a known protein structure and conformations of a mimic, which are spatially superposed with the protein backbone. A compound library with peptidomimetic compounds collected from the literature as well as several protein structure libraries are provided, which can be scanned exhaustively.
Pro-origami is a system for automatically generating protein structure cartoons. The cartoons are intended to make protein structure easy to interpret by laying out the secondary and super-secondary structure in two dimensions in a manner that makes the structure clear.
PDBpaint is a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user.