I have always been a fan of Bowie's lab software and Hotpatch is a great example of web-based tool which is useful for both teaching and research. However, their website ( http://hotpatch.mbi.ucla.edu/ ) is down for some time and I can't find a support contact. What are the good alternatives out there? For those who don't know it, it uses different properties (such as cavities, surface electrostatics, residue usage, hydrophobicity, etc) to predict functional sites related to metal binding, catalysis, protein-protein contact, nucleotide binding, etc.
Maybe not as powerful as Hotpatch but the 3DLigandSite can be useful, looks for conserved structural motifs. It has a database of nucleotide and metal binding sites and looks to see if your protein has any of these. It can be found here;
http://www.sbg.bio.ic.ac.uk/~3dligandsite/
I was not aware of this one - it actually complements hotpatch given that the method is different - and very useful! Thanks a lot.
As for hotpatch, I managed to contact James Bowie and it seems they hit some trouble after moving some servers and that is why hotpatch is down. They're already looking at the issue (the server itself is back, but submissions are not working last time I checked)
There are many. web servers for small ligand binding site prediction. COACH, which combine the four methods below, is rated as the most accurate by the CAMEO blind prediction contest. http://www.cameo3d.org/lb/1-year/ and file below
COACH http://zhanglab.ccmb.med.umich.edu/COACH/
FINDSITE(downloadable) http://cssb.biology.gatech.edu/skolnick/files/FINDSITE
ConCavity (source code available) http://compbio.cs.princeton.edu/concavity/
COFACTOR(can be downloaded through ITASSER) http://zhanglab.ccmb.med.umich.edu/COFACTOR/
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