[BiO BB] Modeling of small peptides

Raghu Prasad Rao, METPALLY raghu at velgonda.cs.qc.cuny.edu
Thu Jan 4 13:17:57 EST 2007

hi shameer,

If you know the homologous peptide fragment with known
structure corresponding your target peptide then using SCWRL program you
can replace side chains and minimize it to get fairly good initial model.

SCWRL is available form Dunbracks lab
Web Server: http://www1.jcsg.org/scripts/prod/scwrl/serve.cgi

or you can also use one of the modules of SYBYL or insightII to model
small peptides.

or use The Dundee PRODRG2 Server

or use DSDBASE to model disulphide rich peptides

all the above and many more softwares are available with different rates
of accuracies.


> Dear All,
> What is the best approach to model small peptides ?
> Is it homology (i think ... no ! ) or ab-initio or any other efficient
> methods or servers / programs available ?
> Please share your knowledge,
> Thanks in advance !!!
> -- 
> S K
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