Bioinformatics (Oxford, England)
Oct 15, 2019
MOTIVATION: Studies have shown that the accuracy of random forest (RF)-based scoring functions (SFs), such as RF-Score-v3, increases with more training samples, whereas that of classical SFs, such as X-Score, does not. Nevertheless, the impact of the...
Journal of bioinformatics and computational biology
Oct 1, 2019
At present, most of the researches on protein classification are based on graph kernels. The essence of graph kernels is to extract the substructure and use the similarity of substructures as the kernel values. In this paper, we propose a novel graph...
Bioinformatics (Oxford, England)
Sep 15, 2019
MOTIVATION: Protein model quality assessment (QA) is a crucial and yet open problem in structural bioinformatics. The current best methods for single-model QA typically combine results from different approaches, each based on different input features...
Bioinformatics (Oxford, England)
Sep 15, 2019
MOTIVATION: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy and interpretability.
Bioinformatics (Oxford, England)
Sep 15, 2019
MOTIVATION: Protein structure refinement aims to bring moderately accurate template-based protein models closer to the native state through conformational sampling. However, guiding the sampling towards the native state by effectively using restraint...
Journal of biosciences
Sep 1, 2019
Protein-protein interactions (PPIs) are important for the study of protein functions and pathways involved in different biological processes, as well as for understanding the cause and progression of diseases. Several high-throughput experimental tec...
Bioinformatics (Oxford, England)
Jul 15, 2019
MOTIVATION: Sequence-based protein-protein interaction (PPI) prediction represents a fundamental computational biology problem. To address this problem, extensive research efforts have been made to extract predefined features from the sequences. Base...
Bioinformatics (Oxford, England)
Jul 15, 2019
MOTIVATION: Sequence-based prediction of one dimensional structural properties of proteins has been a long-standing subproblem of protein structure prediction. Recently, prediction accuracy has been significantly improved due to the rapid expansion o...
Bioinformatics (Oxford, England)
Jul 15, 2019
MOTIVATION: Computational methods for protein post-translational modification (PTM) site prediction provide a useful approach for studying protein functions. The prediction accuracy of the existing methods has significant room for improvement. A rece...
Bioinformatics (Oxford, England)
Jul 15, 2019
MOTIVATION: Domain boundary prediction is one of the most important problems in the study of protein structure and function. Many sequence-based domain boundary prediction methods are either template-based or machine learning (ML) based. ML-based met...