Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features.
BACKGROUND
Adenosine-5'-triphosphate (ATP) is one of multifunctional nucleotides and plays an important role in cell biology as a coenzyme interacting with proteins. Revealing the binding sites between protein and ATP is significantly important to understand the functionality of the proteins and the mechanisms of protein-ATP complex.


RESULTS
In this paper, we propose a novel framework for predicting the proteins' functional residues, through which they can bind with ATP molecules. The new prediction protocol is achieved by combination of sequence evolutional information and bi-profile sampling of multi-view sequential features and the sequence derived structural features. The hypothesis for this strategy is single-view feature can only represent partial target's knowledge and multiple sources of descriptors can be complementary.


CONCLUSIONS
Prediction performances evaluated by both 5-fold and leave-one-out jackknife cross-validation tests on two benchmark datasets consisting of 168 and 227 non-homologous ATP binding proteins respectively demonstrate the efficacy of the proposed protocol. Our experimental results also reveal that the residue structural characteristics of real protein-ATP binding sites are significant different from those normal ones, for example the binding residues do not show high solvent accessibility propensities, and the bindings prefer to occur at the conjoint points between different secondary structure segments. Furthermore, results also show that performance is affected by the imbalanced training datasets by testing multiple ratios between positive and negative samples in the experiments. Increasing the dataset scale is also demonstrated useful for improving the prediction performances.
Department of Automation, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
Ya-Nan
YN
Zhang
Dong-Jun
DJ
Yu
Shu-Sen
SS
Li
Yong-Xian
YX
Fan
Yan
Y
Huang
Hong-Bin
HB
Shen
D000255:Adenosine Triphosphate / Q000737:chemistry*; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry*; D060388:Support Vector Machine
D011506:Proteins; D000255:Adenosine Triphosphate