• Help
• Tools
• FAQs
• Credits
• Benchmarks

3D-footprint is maintained by the Computational & Structural Biology group (Zaragoza, Spain). Early versions of the DNAPROT algorithm were originally conceived at the Center for Genome Sciences (UNAM, Mexico). The database was originally funded by grant CSIC:200720I038 and ARAID. Interface matrix plots were created by CP Cantalapiedra and added in 2012. If you use this resource we ask you to cite the main paper describing this work:

Contreras-Moreira,B. (2010) 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic Acids Research, 38, D91-D97 (PDF)

and to consider citing other relevant papers:

• Espinosa-Angarica et al (2008) Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics, 9:436. (PubMed)
• Morozov AV and Siggia ED. (2007) Connecting protein structure with predictions of regulatory sites. PNAS, 104(17):7068-73. (PubMed)

Further reading:

• Sebastián A, Cantalapiedra CP, Contreras-Moreira B (2012) Interface similarity improves comparison of DNA-binding proteins: the Homeobox example. Lecture Notes in Computer Science, 6620/2012:72-82 (PDF, authors' PDF, suppl)
• Contreras-Moreira B, Sancho J and Espinosa-Angarica V (2009) Comparison of DNA binding across protein superfamilies. Proteins, 78(1):52-62 (PubMed)
• Prabakaran P, Siebers JG, Ahmad S, Gromiha MM, Singarayan MG and Sarai A (2006) Classification of protein-DNA complexes based on structural descriptors. Structure, 14(9):1355-67. (PubMed)

3D-footprint relies on the DNAPROT algorithm, developed in-house, and on several valuable resources: the Protein Data Bank, SCOP, Superfamily, Pfam, BLAST, HMMER, MAMMOTH, STAMP, WEBLOGO, TFmodeller, PHYLIP, Graphviz, PostScript::Simple, matrix2png,STRIDE 3DNA, HBPLUS, SCWRL, PubMed, R and RSA-tools.

Feedback and troubleshooting

Should you have any questions regarding 3D-footprint, please get in touch at compbio@eead.csic.es.

Disclaimer

This service is available AS IS and at your own risk. EEAD-CSIC and CCG-UNAM do not give any representation or warranty nor assume any liability or responsibility for the service or the results posted (whether as to their accuracy, completeness, quality or otherwise). Access to the service is available free of charge for ordinary use in the course of research.