ERA

Download the full-sized PDF of CS23D: A web server for rapid protein structure generation using NMR chemical shifts and sequence dataDownload the full-sized PDF

Analytics

Share

Permanent link (DOI): https://doi.org/10.7939/R39P2W84K

Download

Export to: EndNote  |  Zotero  |  Mendeley

Communities

This file is in the following communities:

Biological Sciences, Department of

Collections

This file is in the following collections:

Journal Articles (Biological Sciences)

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

Descriptions

Author or creator
Wishart, D.S.
Arndt, D.
Berjanskii, M.
Tang, P.
Zhou, J.
Lin, G.
Additional contributors
Subject/Keyword
assignment
predictions
identification
restraints
algorithms
C-13
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
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 0.2–2.8A ° 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
.

Date created
2008
DOI
doi:10.7939/R39P2W84K
License information
Rights
© 2008 The Author(s)
Citation for previous publication
DS Wishart, D Arndt, M Berjanskii, P Tang, J Zhou and G Lin. "CS23D: A web server for rapid protein structure generation using NMR chemical shifts and sequence data." Nucleic Acids Research 36 (Web Server issue) (2008): W496-502. DOI: 10.1093/nar/gkn305
Source
Link to related item

File Details

Date Uploaded
Date Modified
2014-04-25T00:48:26.447+00:00
Audit Status
Audits have not yet been run on this file.
Characterization
File format: pdf (Portable Document Format)
Mime type: application/pdf
File size: 1580911
Last modified: 2015:10:12 16:18:43-06:00
Filename: Nucleic_Acids_Research_36_2008_W496.pdf
Original checksum: aa790bf0b5f86c113ba3930531ba82c5
Well formed: true
Valid: true
File title: gkn305 496..502
Page count: 7
Activity of users you follow
User Activity Date