DDNA specifications


Unique identifier OMICS_17034
Alternative name DDNA3
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3
Stability No
Registration required Yes
Maintained No



Add your version


Unique identifier OMICS_17034
Alternative name DDNA3
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for DDNA


An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles.

2009 Proteins
PMCID: 2743280
PMID: 19274740
DOI: 10.1002/prot.22384

DDNA in publications

PMCID: 5514533
PMID: 28715997
DOI: 10.1186/s12859-017-1755-0

[…] problem limit its ability to capture the key hydrogen bonds and π-interactions that contribute to tf-dna binding specificity []. the ie function improved tfbs prediction accuracy over mb as well as ddna3, a knowledge-based atomic-level protein-dna interaction potential [, , ]. however, the algorithm cannot scale well for prediction of longer tf binding sites, especially for binding sites […]

PMCID: 4908348
PMID: 27307632
DOI: 10.1093/bioinformatics/btw264

[…] highly similar proteins., we applied the new ie function to the prediction of tfbss using the non-redundant dataset of 29 tf–dna complex structures and compared the prediction with mb potential and ddna3, a knowledge-based atomic-level protein–dna interaction potential (). five examples of the predicted tf-binding motifs and the corresponding jaspar motifs are shown in a (all 29 predicted […]

PMCID: 4014986
PMID: 24809456
DOI: 10.1038/srep04907

[…] the step-size of the processive movement were measured at 10 μm atp, which slows down the myosin movement such that the stepping behavior can be analyzed by fiona. the stepping traces of myo5c-hmm-ddna36 are shown in . the histogram of the overall step-size of myo5c-hmm-ddna36 shows a broad distribution with an average of 30.4 ± 7.9 nm (, open triangle with red solid line, mean ± s.d., n = […]

PMCID: 3540023
PMID: 23320072
DOI: 10.1371/journal.pone.0052460

[…] methods further extend the statistical energy function derived with the distance-scaled fire (dfire) state that was originally developed for proteins , and applied to protein/dna interactions (ddna , ddna2 , the energy function obtained by training all non-homology structures in pdb by vcfire). improvements over ddna2 by fire-based energy functions are observed in four different tests: […]

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DDNA institution(s)
Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, China; Indiana University School of Informatics, Indiana University-Purdue University, Indianapolis, Indiana, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
DDNA funding source(s)
Supported by the NIH (GM066049 and GM085003), China Outstanding Youth Fund( No. 20525416), and China Scholarship Council.

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