= Bend.it® Server =
== Introduction ==
This software predicts DNA curvature from DNA sequences. The curvature is
calculated as a vector sum of dinucleotide geometries (roll, tilt and twist angles)
using the BEND algorithm of Godsell and Dickerson, and expressed as degrees per
helical turn (10.5 °/helical turn = 1 °/basepair).
This calculation - like all predictions - is approximate. Experimentally tested
curved motifs produce curvature values of 5 to 25 °/helical turn, while straight
motifs give values below 5 °/helical turn.
Basic concepts, references and tips for evaluation are provided, along with
short examples.
The results are presented in several forms:
a) 1-D sequence plot, in which the curvature and the flexibility or GC content are
plotted along the DNA sequence with options to smooth the plot
b) 2-D plot, in which the curvature is plotted against flexibility or GC content
c) ASCII (text only) tabulated output of calculated values, sent by e-mail.
== Requirements ==
1. GCC
2. Makefile
3. GNUPlot
== Compilation ==
cd bendit
make all
== Web server ==
You can run the program using our web server:
http://pongor.itk.ppke.hu/dna/bend_it.html
== References ==
1. Ligeti B.; Vera R.; Juhász J.; Pongor S. (2016). CX, DPX and PCW (2016): Web
servers for the visualization of interior and protruding regions of protein
structures in 3D and 1D. Prediction of Protein Secondary Structure,
Methods in Molecular Biology. 1484, Chapter 20, 301–310.
2. Vlahovicek, K., Kaján and Pongor, S. (2003): "DNA analysis servers: plot.it.,
bend.it, model.it and IS" Nucleic Acids Res., 31(13), 3686-7
3. Gabrielian, A., Vlahovicek, K. and Pongor S. (1997): "Distribution of
sequence-dependent curvature in genomic DNA" FEBS Letters, 406, 69-74
4. Gabrielian, A., Simoncsits, A. and Pongor, S. (1996): "Distribution of
Bending Propensity in DNA Sequences" FEBS Letters, 393, 124-130
5. Gabrielian, A., Pongor, S. (1996) "Correlation of intrinsic DNA curvature
with DNA property periodicity", FEBS Letters, 393, 65-68
6. Brukner, I., Sanchez, R., Suck, D. and Pongor, S. (1995) "Sequence dependent
bending propensity of DNA as revealed by DNAse I: Parameters for
trinucleotides" EMBO J. 14, 1812-1818.
7. Goodsell, D.S. and Dickerson, R.E. (1994) "Bending and curvature calculations
in B-DNA" Nucl. Acids Res. 22, 5497-5503
== Contact ==
Sándor Pongor, PhD DSc
Professor,
Faculty of Bionics and Information Technology
Pázmány Péter Catholic University
Práter u. 50/a, 1083 Budapest, Hungary
E-mail: pongor.sandor@itk.ppke.hu
Telephone: +36-1-886-4703
Fax: +36-1-886-4724
Roberto Vera Alvarez, PhD
Computational Structural Biologist
MSC & National Center for Biotechnology Information
E-mail: r78v10a07@gmail.com