Stereochemical errors and their implications for molecular dynamics simulations

BMC Bioinformatics

Table 1 Chirality errors and cis peptide bonds in the Protein Data Bank

¹ As given by EXPDTA record on each PDB file. Entries with more than one method were classified based on the first method listed. Only methods with at least 100 solved structures are shown in the table.
2 Total number of chirality errors or cis peptide bonds detected by the Chirality and Cispeptide VMD plugins, respectively.
³ Total number of residues divided by total number of chirality errors or cis peptide bonds. For chirality errors, all protein and nucleic acid residues are counted; for cis peptide bonds, only protein residues are counted.
⁴ For chirality, only structures containing at least one protein or nucleic acid residue were considered. For cis peptide bonds, only structures containing at least one peptide bond were kept in the analysis.

ISSN: 1471-2105