What is CFG Analysis?

CFG Analysis ^{1, 2} is a general method for predicting the location of functionally important sites within a target protein structure. Like other available structure/sequence analysis techniques, CFG Analysis exploits the evolutionary relationships present across groups of homologous proteins to identify regions that are likely to be of functional significance. However, this technique is particularly useful for situations where other methods fail, for instance when only a few or highly similar homologues can be identified. In such cases, a preliminary identification of functionally important sites may be coupled to a more detailed analysis of these regions with techniques that map evolutionarily conserved residues onto protein surfaces - such as Evolutionary Trace (ET) Analysis ^{3, 4, 5, 6} or ConSurf.⁷

---

---

How to Use this Server

The siteFiNDER|3D Server requires, at a minimum, a query protein of known structure with coordinates in standard PDB format. In addition, a multiple sequence alignment in modified PIR format featuring homologues of the query protein may either be provided or generated automatically from sequences accumulated by the server.

To begin using the server, click the "Start New Session" button above. Alternatively, you may wish to read our list of Frequently Asked Questions.

Sequence Extractor

The following tool may be used to ensure that the multiple sequence alignment entry corresponding to the query structure is formatted correctly. If you are providing your own alignment, simply copy and paste the sequence returned by the server into your list of sequences prior to aligning them.

Upload PDB file for extraction:

---

References

Papers Related to CFG Analysis

• 1. Innis, C.A. (2007). siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins. Nucl. Acids Res. 35 (Web Server Issue), W489-494 (PubMed).
• 2. Innis, C.A., Anand, A.P., Sowdhamini, R. (2004). Prediction of functional sites in proteins using Conserved Functional Group analysis. J. Mol. Biol. 337, 1053-1068 (PubMed).

Links to Other Functional Site Prediction Servers

• 3. Evolutionary Trace Server (Lichtarge Computational Biology Lab, BCM)
• 4. Jevtrace2 (The Cohen Group, UCSF)
• 5. TraceSuite II Server (Cambridge)
• 6. Evolutionary Trace Server (Osaka)
• 7. Consurf Server

---

For comments, suggestions or to report any problems with the server, please send a message to "axel.innis {at} yale.edu".