Tuesday, May 18, 2010

B Fwd: [WebBio] PepStr

---------- Forwarded message ----------
From: "Raghava" <>
Date: May 18, 2010 12:41 PM
Subject: [WebBio] PepStr
To: "webbio: Web Servers for Biologists" <>

Name: PepStr

Pepstr is a de novo method for prediction of tertiary structure of
small peptides. It uses 3 steps:
In first step, the regular secondary structure states (helix, β-strand
and coil) and β-turn types are predicted using BetaTurns method.
Secondly, initial or starting conformation for a given sequence is
generated using the Tleap module of Amber version6 with phi, psi
values corresponding to the secondary structure states predicted in
step I. The side chain angles are asigned using standard Dunbrack
backbone dependent rotamer library.
This initial conformation is then subjected to energy minimization and
molecular dynamics simulations using Sander module of Amber. It
consists of few initial cycles of steepest descent minimization
followed by dynamics which is carried out for 25ps at 300K using 1-fs
time steps. Finally, this is followed by minimization using a
combination of steepest descent and cojugate gradient algorithms.
The final coordinates are saved in PDB format.