TY - GEN
T1 - Prediction of DNA-binding propensity of proteins by the ball-histogram method
AU - Szabóová, Andrea
AU - Kuželka, Ondřej
AU - Morales E., Sergio
AU - Železný, Filip
AU - Tolar, Jakub
PY - 2011/5/16
Y1 - 2011/5/16
N2 - We contribute a novel, ball-histogram approach to DNA-binding propensity prediction of proteins. Unlike state-of-the-art methods based on constructing an ad-hoc set of features describing the charged patches of the proteins, the ball-histogram technique enables a systematic, Monte-Carlo exploration of the spatial distribution of charged amino acids, capturing joint probabilities of specified amino acids occurring in certain distances from each other. This exploration yields a model for the prediction of DNA binding propensity. We validate our method in prediction experiments, achieving favorable accuracies. Moreover, our method also provides interpretable features involving spatial distributions of selected amino acids.
AB - We contribute a novel, ball-histogram approach to DNA-binding propensity prediction of proteins. Unlike state-of-the-art methods based on constructing an ad-hoc set of features describing the charged patches of the proteins, the ball-histogram technique enables a systematic, Monte-Carlo exploration of the spatial distribution of charged amino acids, capturing joint probabilities of specified amino acids occurring in certain distances from each other. This exploration yields a model for the prediction of DNA binding propensity. We validate our method in prediction experiments, achieving favorable accuracies. Moreover, our method also provides interpretable features involving spatial distributions of selected amino acids.
UR - http://www.scopus.com/inward/record.url?scp=79955869476&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79955869476&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-21260-4_34
DO - 10.1007/978-3-642-21260-4_34
M3 - Conference contribution
AN - SCOPUS:79955869476
SN - 9783642212598
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 358
EP - 367
BT - Bioinformatics Research and Applications - 7th International Symposium, ISBRA 2011, Proceedings
T2 - 7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011
Y2 - 27 May 2011 through 29 May 2011
ER -