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DR_bind, The DNA-Binding Residue Prediction Server

Yao-Chi Chen1, Jon Wright1,2 and Carmay Lim1,3

1Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
2Genomics Research Center, Academia Sinica, Taipei, Taiwan
3Department of Chemistry, National TsingHua University, HsinChu, Taiwan

This server can be used to predict the DNA-binding residues for a given protein chain using the algorithm published in Chen et al. 2007†, which is summarized on this page. For your target protein complete the following steps to receive a prediction of the DNA-binding residues for your protein chain. (Note: Currently we are taking only single chain PDB structures).

The button below automatically loads the data needed to do a DNA binding residue prediction for 1TSR, chain B, or if you wish you can just look at the output that was given from a saved prediction we did earlier. It may take up to ten seconds for the data to be downloaded and for the prediction to start, which usually takes about 90 minutes.

Output from a previous prediction on chain B from 1TSR can be found here.

Choose either option A or option B (Help)

Option A) For single protein chain structures that are to be uploaded from files.
Step A1: Upload the structure of your target protein with standard PDB file format. (Example)
Step A2: Upload the prepared evolution information of your target protein in ConSurf format, if available. (Example)
Step A3: Automatically generate evolutionary data if possible (ignored if a ConSurf file is uploaded).

 

Option B) For known PDB archive entries with multiple protein chains

The server will check for and retrieve the ConSurf data information automatically if it has been precalculated in the ConSurf-DB; if it has not, it will attempt to generate the ConSurf data automatically. If no ConSurf data can be generated, the prediction will continue and you will be informed of the missing ConSurf data on the Results page. (Help)
Step B1: Enter the PDB ID code.  E.g. 1tsr
Step B2: Enter the chain assignment letter.  E.g. A
Step B3: Use evolutionary data if available (recommended).

 

Submission
Optional Step: Optional: If you would like an email saying when your results are ready please enter an email address, however you do not have to enter anything here.
Submission Step: Click on the submit button to send to the DNA-binding residue prediction server, it may take 10 seconds while we check your input. Results will be kept for 2 months. (Help)
Multiple Submissions: You may use the multiple prediction submission form for predictions on many different single chains.

References and programs used in creating this server.

If you use DR_bind for predicting DNA-binding residues please cite both Chen et al. 2012 and Chen et al. 2007.

†Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation, Chen Y-C, Wu C-Y and Lim C. (2007) Proteins, 67, 671-80. PubMed

DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry Y-C Chen, J.D. Wright and C. Lim (2012) Nucleic Acids Research, 40. PubMed

AMBER D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B.P. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2010), AMBER 11, University of California, San Francisco. PubMed

CONSURF ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Ashkenazy H., Erez E., Martz E., Pupko T. and Ben-Tal N. (2010) Nucleic Acids Research, 38, W529-533. PubMed

ConSurf-DB The ConSurf-DB: Pre-calculated evolutionary conservation profiles of protein structures. Goldenberg O., Erez E., Nimrod G and. Ben-Tal N. (2009) Nucleic Acids Research, 37, Database issue D323-D327. PubMed

HBPLUS Satisfying Hydrogen Bonding Potential in Proteins. McDonald I.K. and Thornton J.M. (1994) JMB, 238, 777-793. PubMed

SCWRL Improved prediction of protein side-chain conformations with SCWRL4. Krivov G.G., Shapovalov M.V. and Dunbrack R.L. Jr. (2009) Proteins, 77, 778-795. PubMed

MOLMOL MOLMOL: A program for display and analysis of macromolecular structures,  Koradi R., Billeter M. and Wuthrich K. (1996) Journal of molecular graphics, 14, 51-55. PubMed

DR_bind is hosted at The Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.