Hi Hugh, Waltz is an excellent web-server to give very good results on amyloidogenic regions based on sequence stretches (correlate the regions with hydrophobic patches by hydropathy plot obtained from Expassy-Protscale). Aggrescan and PASTA are two other reliable servers for the same kind of prediction (though I have more preference for Waltz). Based on the 3D structure (pdb structures) you can use the Maestro program (from Schrodinger Inc.) to get the aggregation prone surface(s) / aggregation prone surface regions.
Best!! Debasish CSIR- Senior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html ----- Original Message ----- From: "Hugh Morgan" <00001103e90ebb53-dmarc-requ...@jiscmail.ac.uk> To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, July 26, 2017 10:35:07 PM Subject: [ccp4bb] Hydrophobic hotspots Hi all, can anyone recommend a program for identifying hydrophobic (aggregation) hotspots using either the amino acid sequence and/or structural data. Thanks in advance for your help Hugh Ps. Have tried aggrescan but would like to try a few others and compare, ideally a more structural based program.
