Tools for Functional Annotation
Understanding the function of a protein is fundamental if we wish to have a better understanding of biology and disease. Many structural and functional analysis tools have been developed by the PSI to give us a peek into some of this information. Community annotation servers have also been set up to engage the greater scientific community to work with us.
PSI-developed tools for functional analysis and prediction
- The Global Protein Surface Survey (GPSS) server at PSI MCSG provides analysis of all MCSG functionally annotated surfaces. Annotation can be viewed through the GPSS web interface or using a plug-in to the PyMOL molecular visualization program.
- The MarkUs Functional Annotation Server at PSI NESG is a web server to assist the assessment of the biochemical function for a given protein structure. MarkUs identifies related protein structures and sequences, detects protein cavities, and calculates the surface electrostatic potentials and amino acid conservation profile.
- The ProFunc server (developed by the PSI MCSG and EBI) identifies likely biochemical function of a protein from its three-dimensional structure. This has been done for PSI MCSG structures.
- The Tempura server performs a reverse template analysis on the results from ProFunc (PSI MCSG)
- The Open Protein Structure Annotation Network (TOPSAN) at PSI JCSG is a wiki-based project where automated target annotations are integrated with structure determination summary reports extracted from the JCSG database. TOPSAN provides access to outside collaborators to comment on and/or annotate a structure through an open mechanism similar to Wikipedia.
- The NESG Functional Annotation Server at PSI NESG provides functional annotation of solved NESG structures including multiple sequence alignments (ClustalW), sequence homologs (PSI-Blast), domain assignments (InterPro, Pfam), structure alignment (Dali, SKAN), and cavity analysis (SCREEN).