DDNA statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool DDNA
info

Tool usage distribution map

info info

Associated diseases

info

Popular tool citations

chevron_left Transcription factor binding site prediction Protein-DNA interaction prediction chevron_right
Want to access the full stats & trends on this tool?

DDNA specifications

Information


Unique identifier OMICS_17034
Name DDNA
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

Download


download.png

Versioning


No version available

Information


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

Publication for DDNA

library_books

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 citations

 (2)
library_books

An efficient algorithm for improving structure based prediction of transcription factor binding sites

2017
BMC Bioinformatics
PMCID: 5514533
PMID: 28715997
DOI: 10.1186/s12859-017-1755-0

[…] t 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 from TF […]

library_books

Creating PWMs of transcription factors using 3D structure based computation of protein DNA free binding energies

2010
BMC Bioinformatics
PMCID: 2879287
PMID: 20438625
DOI: 10.1186/1471-2105-11-225

[…] aving the largest AUC of 0.956 ± 0.002 followed by the PWM from Ref. [] compiled from 100 experimentally verified p53 response elements, having AUC of 0.921 ± 0.003. The p53 PWM recalculated with the DDNA2 server and the corresponding TRANSFAC matrix performed quite comparable (AUC of 0.901 ± 0.007 and 0.902 ± 0.006, respectively). In this Figure, the p53 PWM developed here showed somehow smaller […]


Want to access the full list of citations?
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.

DDNA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review DDNA