The role of DNA deformation energy at individual base steps for the identification of DNA-protein binding sites.
We examine the use of deformation propensity at individual base steps for the identification of DNA-protein binding sites. We have previously demonstrated that estimates of the total energy to bend DNA to its bound conformation can partially explain indirect DNA-protein interactions. We now show that the deformation propensities at each base step are not equally informative for classifying a sequence as a binding site, and that applying non-uniform weights to the contribution of each base step to aggregate deformation propensity can greatly improve classification accuracy. We show that a perceptron can be trained to use the deformation propensity at each step in a sequence to generate such weights.
Department of Information and Computer Science, University of California, Irvine, CA 92697, USA. nsteffen@uci.edu
Nicholas R
NR
Steffen
Scott D
SD
Murphy
Richard H
RH
Lathrop
Michael L
ML
Opel
Lorenzo
L
Tolleri
G Wesley
GW
Hatfield
D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000378:metabolism*; D008958:Models, Molecular; D016571:Neural Networks, Computer; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013816:Thermodynamics
D011506:Proteins; D004247:DNA