[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.
Re: [ccp4bb] Hydrophobic hotspots
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" <1103e90ebb53-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.
Re: [ccp4bb] Hydrophobic hotspots
Dear Morgan Protein aggregation surface module in schrodinger could generate aggregation hotspots. Regards Mahesh From: CCP4 bulletin board on behalf of Hugh Morgan <1103e90ebb53-dmarc-requ...@jiscmail.ac.uk> Sent: Wednesday, July 26, 2017 8:05 PM To: CCP4BB@JISCMAIL.AC.UK 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.
Re: [ccp4bb] Hydrophobic hotspots
Dear Hugh If you know Aggrescan then I assume you're away of its 3D counterpart? http://biocomp.chem.uw.edu.pl/A3D/ It even allows you to consider whether structures reached by coarse-grained MD are more aggregation-prone than your starting structure. Good luck Daniel On 26/07/17 18:05, Hugh Morgan wrote: 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. -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 Institute of Integrative Biology FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool http://pcwww.liverpool.ac.uk/~drigden/ Crown St., Liverpool L69 7ZB, U.K.
Re: [ccp4bb] Hydrophobic hotspots
Hi, You can try the following using protein structures: 1) https://sbgrid.org/software/titles/quilt 2) Swiss PDBViewer, detect hydrophobic patches under Tool Surface 3) EBI PISA and look for negative delta G 4) look at protein-protein interaction and interface dbases Best, Debanu > On Jul 26, 2017, at 10:05 AM, Hugh Morgan > <1103e90ebb53-dmarc-requ...@jiscmail.ac.uk> wrote: > > 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.
