CHAINTWEAK: Sampling From The Neighbourhood of a Protein Conformation
Speaker: Rohit Singh , Computation & Biology Group at CSAIL, MIT
Date: April 4 2005
Time: 11:30AM to 1:00PM
Location: TOC LAB 32-G575
Host: P Clote/ BC & B Berger/ MIT, MIT- Dept of Mathematics, CSAIL & HST
Contact: Kathleen Dickey, 617 253-3037, kvdickey@mit.edu
Relevant URL: http://www-math.mit.edu/compbiosem/When searching for an optimal protein structure, it is often necessary to
generate a set of structures similar to a base structure (e.g., within 4A
Root Mean Square Deviation (RMSD)). Current methods to do this are
designed to produce only small deviations (< 0.1A RMSD) and are
inefficient for larger deviations. The method proposed in this paper,
ChainTweak, can generate conformations with larger deviations from the
base much more efficiently. For example, in 18 seconds it can generate 100
backbone conformations, each within 1-4A RMSD of a given 45-residue
conformation. Moreover, each conformation has correct bond lengths, angles
and omega torsional angles; its phi-psi angles have energetically
favorable values; and there are rarely any backbone steric clashes. The
method uses the insight that loop closure techniques can be used to
perform compensatory changes of dihedral angles so that only a part of the
conformation is changed. It is demonstrated, using decoys from the Decoys
`R Us data-set, that ChainTweak can be used to construct good decoys. It
also provides a novel and intuitive way of analyzing the energy landscape
of a protein. In addition, ChainTweak can improve the accuracy and
performance of the loop modeling program RAPPER by an order of magnitude
(1.1 min. vs. 36 min. for an 8-residue chain).
MIT
Department of Mathematics
& The Theory of
Computation Group
At CSAIL
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