In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30) protein structures distinct from the training...

Source code can be treated similar as corpus constructed by natural language (Hindle et al., 2012). In this paper, we use the neural network model to study identifer naming convention problem. We find that neural network model can predict 16.5% identifiers correctly on a randomlyselected source file by training on the unrelated projects. In addition, we compare the performance of model on chara...