Protein sidechain conformer prediction: a test of the energy function

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Erratum Protein sidechain conformer prediction: a test of the energy function Robert J Petrella, Themis Lazaridis and Martin Karplus Folding & Design 30 September 1998, 3:353–377

On page 366, first paragraph, the fourth sentence should read as follows: The results indicate that the conformers around (χ1,χ2) = (χ1, 40° or 45°) and (χ1 + 45°, 195° or 200°) are the most nearly symmetric or pseudosymmetric pairs. On page 356, the bottom row of Table 3 should appear as follows:

Table 3

c1 ×´ χc2 rotations by residue type. Number of correctly predicted residues for χ All residues Amino acid type

Number of residues

All

1142

χ1 991

%

Core residues χ2|χ1

Number of residues

%‡

564

574

χ1 545

%

χ2|χ1

%

347

On page 362, Figure 3, there should be visible a single sidechain with 12 alternative minima within 10 kcal/mol as follows:

Figure 3 90 ∆E < 5 kcal/mol ∆E < 10 kcal/mol

80

Number of residues

70 60 50 40 30 20 10 0

0

1

2 3 4 5 6 7 8 9 10 11 Number of minima within given tolerance of primary minimum

12

Folding & Design

Histogram of the distribution of energies in the relative minima occurring in sidechain dihedral energy maps of thermolysin. The plot counts minima of rank two and lower for sidechains having at least two heavy-atom dihedral angles. Degenerate χ2 conformers in phenylalanine and aspartate are excluded. 52% and 76% of all residues have at least one local minimum within 5 kcal/mol and 10 kcal/mol, respectively, of their absolute minima.