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): [log in to unmask], [log in to unmask]
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" <[log in to unmask]>
To: [log in to unmask]
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.
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