Illustration of the definition of probabilist maps for Poisson-Boltzmann calculation. Let us consider a toy protein consisting of two amino acids, i and m, that can both adapt one of the two possible conformations, or rotamers. The two rotamers for amino acid i are assigned weights P(i, 1) and P(i, 2) such that P(i, 1) + P(i, 2) = 1. The corresponding multi-copy system is shown on the left, overlaid on a Cartesian grid. As the two conformations for amino acid i are independent realization of the side-chain position, the probability ρ i (S) that amino acid i covers a site S is simply the weighted sum of the probabilities ρ i1(S) and ρ i2(S) of each of its conformations covering S (A). The same applies for amino acid m (B). As i and m co-exist in the protein, the probability γ solv (S) that site S remains “uncovered,” i.e., accessible to solvent, is given by a product rule (C).
Effects of adding the electrostatic free energy as computed by PB in the SCMF functional free energy on side-chain prediction accuracy. The dihedral angles χ1 and χ2 are considered to be correctly predicted if their values are within 40° of their reference values in the native structures.
The accuracy with which the dihedral angles χ1 of all residues in the DRESS database are predicted is plotted as a function of the accessibility of the residue to solvent, for the SCMF calculation with (continuous line) and without (dashed line) the PB solvation free energy.
The accuracy of SCMF-PB is compared to those of other side-chain prediction programs for a range of side-chain accessibility S (in %).
CPU time required for predicting the conformations of all side chains of a protein versus the number of residues of the protein on a log-log scale, for different methods. The slope of the fitted lines are 0.1, 0.6, 0.98, 1.0, 1.3, and 1.6 for SCMF-PB, TREEPACK, SCAP, OPUS, SCWRL4, and SCMF, respectively.
The SCMF-PB method for predicting side-chain conformations
Improvement of SCMF-PB over SCMF.
Accuracy of SCMF-PB compared to other methods.
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