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DR_bind1, The DNA and RNA Binding Residue Prediction Server

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. It can also use a method capable of predicting both DNA and RNA-binding residues using the method published in Chen et al. 2014 and is summarized on this page. For your target protein complete the following steps to receive a prediction of the NA-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 1HCR, chain A, or if you wish you can just look at the output that was given from a saved prediction we did earlier for 1TSR chain B. After clicking the button it may take up to ten seconds for the data to be downloaded and for the prediction to start, and it will finish in around 5 minutes.

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

Choose prediction method, 2007 for DNA only, 2014 for either RNA or DNA. (Help)

2007 (Recommended for DNA)
2014 (RNA or DNA)

Now provide the protein chain using either option A or option B (Help)

Option A) For single protein chain structures that are to be uploaded from text 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)
Or: Automatically generate evolutionary data if possible (ignored if a ConSurf file is uploaded).
Step A3: For 2014 method preditions only, upload the prepared SAS information of your target protein in SAS format, if available. (Example)
Or: Automatically generate SAS data if possible (only applies to 2014 method predictions, ignored if a SAS 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. For 2014 method binding predictions the server will also attempt to download the SAS data, if none can be located then the prediction will stop and offer advise for continuing. (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).



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 or RNA 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_bind1 for predicting DNA binding residues using the 2007 method please cite both Chen et al. 2012 and Chen et al. 2007, for DNA or RNA predictions using the 2014 method please cite Chen et al. 2014.

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 Chen Y-C, Wright J.D. and Lim C. (2012) Nucleic Acids Research, 40. PubMed

Identifying RNA-binding residues based on evolutionary conserved structural and energetic features Chen Y-C., Sargsyan K., Wright J., Huang Y-S and Lim C. (2014) Nucleic Acids Research, 42. 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

NACCESSS NACCESS - Accessibility calculations.  Hubbard S.J. and Thornton J.M. (1993). Department of Biochemistry and Molecular Biology, University College London, NACCESS

MAPSCI Multiple structure alignment and consensus identification for proteins,  Ilinkin I., Ye J. and Janardan R. (2010) BMC Bioinformatics, 11, 71. PubMed

SAS Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis. Milburn D., Laskowski R.A. and Thornton J.M. (1998) Prot. Eng., 11, 855-859. PubMed

Clustal W Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Thompson J.D., Higgins D.G. and Gibson T.J. (1994) Nucleic Acids Research, 22, 4673-4680. PubMed

CD-HIT Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Li W. & Godzik A. (2006) Bioinformatics, 22, 1658-1659. PubMed

CD-HIT CD-HIT: accelerated for clustering the next generation sequencing data. Fu L., Niu B., Zhu Z. Wu S. and Li W., (2012) Bioinformativs, 28, 3150-3152. PubMed

JSmol JSmol: an open-source HTML5 viewer for chemical structures in 3D. Homepage

DR_bind1 is hosted at The Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.