CS23D -- chemical shift to 3D structure
URL:
What you can do:
A web server for rapid protein structure generation using NMR chemical shifts and sequence data.
Highlights:
- CS23D is a web server for rapidly generating accurate 3D protein structures using only assigned nuclear magnetic resonance (NMR) chemical shifts and sequence data as input.
- Unlike conventional NMR methods, CS23D requires no NOE and/or J-coupling data to perform its calculations.
- CS23D accepts chemical shift files in either SHIFTY or BMRB formats, and produces a set of PDB coordinates for the protein in about 10-15 min.
- CS23D uses a pipeline of several preexisting programs or servers to calculate the actual protein structure.
- Depending on the sequence similarity (or lack thereof) CS23D uses either (i) maximal subfragment assembly (a form of homology modeling), (ii) chemical shift threading or (iii) shift-aided de novo structure prediction (via Rosetta) followed by chemical shift refinement to generate and/or refine protein coordinates.
- Tests conducted on more than 100 proteins from the BioMagResBank indicate that CS23D converges (i.e. finds a solution) for >95% of protein queries.
- These chemical shift generated structures were found to be within 0.2-2.8 A RMSD of the NMR structure generated using conventional NOE-base NMR methods or conventional X-ray methods.
- The performance of CS23D is dependent on the completeness of the chemical shift assignments and the similarity of the query protein to known 3D folds.
Keywords:
- protein structure
- NMR chemical shifts
- 3D protein structure
- 3D folds
- 3D structure
Literature & Tutorials:
This record last updated: 07-29-2008