IEEE/ACM transactions on computational biology and bioinformatics
Jul 23, 2018
Most past works for DNA-binding residue prediction did not consider the relationships between residues. In this paper, we propose a novel approach for DNA-binding residue prediction, referred to as EL_LSTM, which includes two main components. The fir...
International journal of molecular sciences
Jul 16, 2018
Amyloid is an insoluble fibrous protein and its mis-aggregation can lead to some diseases, such as Alzheimer's disease and Creutzfeldt⁻Jakob's disease. Therefore, the identification of amyloid is essential for the discovery and understanding of disea...
Journal of computer-aided molecular design
Jul 10, 2018
We assess the ability of our convolutional neural network (CNN)-based scoring functions to perform several common tasks in the domain of drug discovery. These include correctly identifying ligand poses near and far from the true binding mode when giv...
Biocuration in the omics sciences has become paramount, as research in these fields rapidly evolves towards increasingly data-dependent models. As a result, the management of web-accessible publicly-available databases becomes a central task in biolo...
Protein secondary structure prediction is one of the most important and challenging problems in bioinformatics. Machine learning techniques have been applied to solve the problem and have gained substantial success in this research area. However ther...
IEEE journal of biomedical and health informatics
Jun 12, 2018
Predicting the protein-protein interactions (PPIs) has played an important role in many applications. Hence, a novel computational method for PPIs prediction is highly desirable. PPIs endow with protein amino acid mutation rate and two physicochemica...
Machine learning methods for protein function prediction are urgently needed, especially now that a substantial fraction of known sequences remains unannotated despite the extensive use of functional assignments based on sequence similarity. One majo...
The possibility of using the atomic coordinates of protein-ligand complexes to assess binding affinity has a beneficial impact in the early stages of drug development and design. From the computational view, the creation of reliable scoring functions...
Understanding the genetic basis of complex diseases is challenging. Prior work shows that disease-related proteins do not typically function in isolation. Rather, they often interact with each other to form a network module that underlies dysfunction...
The GO-Cellular Component (GO-CC) ontology provides a controlled vocabulary for the consistent description of the subcellular compartments or macromolecular complexes where proteins may act. Current machine learning-based methods used for the automat...