Extending the accuracy limits of prediction for side-chain conformations.
Current techniques for the prediction of side-chain conformations on a fixed backbone have an accuracy limit of about 1.0-1.5 A rmsd for core residues. We have carried out a detailed and systematic analysis of the factors that influence the prediction of side-chain conformation and, on this basis, have succeeded in extending the limits of side-chain prediction for core residues to about 0.7 A rmsd from native, and 94 % and 89 % of chi(1) and chi(1+2 ) dihedral angles correctly predicted to within 20 degrees of native, respectively. These results are obtained using a force-field that accounts for only van der Waals interactions and torsional potentials. Prediction accuracy is strongly dependent on the rotamer library used. That is, a complete and detailed rotamer library is essential. The greatest accuracy was obtained with an extensive rotamer library, containing over 7560 members, in which bond lengths and bond angles were taken from the database rather than simply assuming idealized values. Perhaps the most surprising finding is that the combinatorial problem normally associated with the prediction of the side-chain conformation does not appear to be important. This conclusion is based on the fact that the prediction of the conformation of a single side-chain with all others fixed in their native conformations is only slightly more accurate than the simultaneous prediction of all side-chain dihedral angles.
Xiang
Z
Z
Department of Biochemistry and Molecular Biophysics BB221, Columbia University, New York, NY 10032, USA.
Honig
B
B
D019295:Computational Biology / Q000379:methods*; D019992:Databases as Topic; D019151:Peptide Library; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results; D012399:Rotation; D012680:Sensitivity and Specificity; D012984:Software; D013816:Thermodynamics
D019151:Peptide Library; D011506:Proteins