The protein side-chain conformation problem calls for predicting protein side-chain structures when their backbone structures are known. This problem plays a very important role in the study of protein structure and function. It has become a key problem in the context of many methods that predict protein folding, and has important applications in designing protein sequences with novel functions.
The protein side-chain amino acids interact energetically with the
protein backbone as well as themselves. It is commonly assumed
that each amino acid residue can take three-dimensional positions
from amongst a finite set of statistically significant
conformations known as rotamers. It is also assumed that
proteins fold in a way that corresponds to a globally minimal energy
conformation, i.e., a conformation that minimizes the total
energy of interaction between residues and between residues and
the protein backbone. Then, the side-chain conformation prediction
problem becomes a combinatorial
optimization problem for the selection of rotamers that minimize
the total energy of interaction. This optimization problem is solved by the R3 online server
using the algorithm developed in
Wei Xie and Nikolaos V. Sahinidis,
Residue-rotamer-reduction algorithm for the protein side-chain conformation problem,
Bioinformatics, 22(2), 188-194, 2006.
Please contact Professor Nick Sahinidis if you have any comments or suggestions.
To Nick Sahinidis' Bioinformatics Software Web SiteTo Nick Sahinidis' Optimization Group Web Site