Protein (Structure) Comparison, Knowledge, Similarity and Information

ProCKSI is a decision support system for protein structure comparison. It integrates several different structural similarity measures (currently CE, FAST, USM, MaxCMO, DaliLite, TM-align, URMS and Vorolign) and compares a set of protein structures against a single target protein or against each other. It also allows the use of user-defined similarity matrices supplementing the build-in methods.

In order to provide a multicriteria view of a set of protein structures, ProCKSI computes a consensus measure based on the chosen set of similarity measures. The results can be further analysed using clustering algorithms and visualised as phenogramsm or validated against the SCOP database using ROC curve analysis.

ProCKSI is running in a distributed environment and is able to perform a large number of comparisons in a short time. It also links to many external resources where more information about protein structures can be found.