NQ-Flipper -- recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
What you can do:
Detect and correct erroneous Asn and Gln rotamers.
Highlights:
- he current Protein Data Bank (PDB) contains about 40 000 protein structures with approximately half a million incorrect atom positions resulting from erroneously assigned asparagine (Asn) and glutamine (Gln) rotamers.
- These errors affect applications in protein structure analysis, modeling and docking and therefore the detection, correction and prevention of such errors is highly desirable.
- We present NQ-Flipper, a web service based on mean force potentials to automatically detect and correct erroneous Asn and Gln rotamers.
- The service accepts protein structure files formatted in PDB style or PDB codes.
- For an Asn/Gln side-chain amide NQ-Flipper computes the total interaction energy with the surrounding atoms as the sum of pairwise atom-atom interaction energies.
- The energy difference between the original and the alternative rotamers identifies the correct configuration of the amide group.
- The web service lists the interaction energies of all Asn/Gln residues found in a PDB file and shows the structure and offending residues in an interactive 3D viewer.
- The corrected protein structure is available for download in various compression formats.
Keywords:
- Asparagine
- Crystallography
- Glutamine
- Molecular Conformation
- Protein Conformation
- Protein Folding
- Reproducibility of Results
- Thermodynamics
- Asn
- Gln
- rotamers
- protein structure analysis
- errors
- error
Literature & Tutorials:
This record last updated: 06-04-2008