DNAgenie (DNA-type specific predictor of DNA-binding residues in protein sequences)

DNAgenie is a webserver that identifies ADNA-, BDNA- and single stranded DNA-binding residues in the protein sequences.

Please follow the three steps below to make predictions:

1. Copy and paste protein sequence(s) into text area

The server accepts up tp 5 FASTA formatted protein sequences between minimum length of 21 residues and maximum length of 5000 residues. Please enter protein sequence(s) in the following text field.

2. Provide your email address (optional)

Please enter your email address in the following text area or leave it blank. A link to prediction results will be sent to your email address once they are ready.

3. Predict

Click button to launch prediction.

Help

The webserver accepts a single protein sequence as the input. The user should submit the protein sequence in the FASTA format.

The format of the input file is as follows:

Line1: >protein ID
Line2: protein sequence (1-letter amino acid encoding)

Here is an example input file.

Materials

Training set: Click here to download
Test set : Click here to download
Human DNA-binding dataset: Click here to download
Supporting Information: Click here to download

References

Upon the usage the users are requested to use the following citation:

Zhang J, GHADERMARZI S, KATUWAWALA A, Kurgan L, 2021. DNAgenie: Accurate Prediction of DNA Type Specific Binding Residues in Protein Sequences. Briefings in Bioinformatics, doi: 10.1093/bib/bbab336

Acknowledgments

We acknowledge with thanks the following software used as a part of this server:

ASAquick - Fast neural network-based predictor of solvent accessibility
HHBlits - Algorithm for homology detection by iterative HMM-HMM comparison
PSIPRED - Prediction of secondary structure
IUPred - Prediction of Intrinsically Unstructured Proteins