Online Server for the Protein Side-Chain Conformation Problem

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. (abstract, paper, bibtex entry)