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. 2008 Jul 1;36(Web Server issue):W496-502.
doi: 10.1093/nar/gkn305. Epub 2008 May 30.

CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data

David S Wishart  1 , David Arndt, Mark Berjanskii, Peter Tang, Jianjun Zhou, Guohui Lin
Affiliations

CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data

David S Wishart et al. Nucleic Acids Res. .

Abstract

CS23D (chemical shift to 3D structure) 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. CS23D is accessible at http://www.cs23d.ca.

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Figures

Figure 1.
Figure 1.
A flow chart outlining the general structure of the CS23D web server and the programs that it calls to generate protein structures from chemical shift data. The specific function of each of the named programs (THRIFTY, PEPMAKE, ROSETTA, etc.) is explained in the text.
Figure 2.
Figure 2.
An illustration of how chemical shift minimization can improve the structure of a poorly modeled initial structure. This shows the improvement seen in a deliberately distorted model of ubiquitin. In this case, the protein regains much of its lost secondary structure and the RMSD converges from 2.5 to 1.0 Å from the native structure.
Figure 3.
Figure 3.
A scatter plot showing the performance of CS23D's three approaches to structure generation (subfragment assembly + homology modeling, chemical shift threading and ab initio structure generation) relative to the level of sequence identity of the matching templates or subfragments. Data from Tables 3–6 in the CS23D web Documentation pages were used to assemble this graph.
See this image and copyright information in PMC

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