International journal of molecular sciences
Jun 15, 2018
Antioxidant proteins can be beneficial in disease prevention. More attention has been paid to the functionality of antioxidant proteins. Therefore, identifying antioxidant proteins is important for the study. In our work, we propose a computational m...
As of April 2018, UniProtKB has collected more than 115 million protein sequences. Less than 0.15% of these proteins, however, have been associated with experimental GO annotations. As such, the use of automatic protein function prediction (AFP) to r...
Residue solvent accessibility is closely related to the spatial arrangement and packing of residues. Predicting the solvent accessibility of a protein is an important step to understand its structure and function. In this work, we present a deep lear...
Lysine glutarylation is new type of protein acylation modification in both prokaryotes and eukaryotes. To better understand the molecular mechanism of glutarylation, it is important to identify glutarylated substrates and their corresponding glutaryl...
It has recently been claimed that the outstanding performance of machine-learning scoring functions (SFs) is exclusively due to the presence of training complexes with highly similar proteins to those in the test set. Here, we revisit this question u...
Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO,...
Determining the catalytic residues in an enzyme is critical to our understanding the relationship between protein sequence, structure, function, and enhancing our ability to design novel enzymes and their inhibitors. Although many enzymes have been s...
Computational and mathematical methods in medicine
Jan 30, 2018
We propose a novel method that predicts binding of G-protein coupled receptors (GPCRs) and ligands. The proposed method uses hub and cycle structures of ligands and amino acid motif sequences of GPCRs, rather than the 3D structure of a receptor or si...
Membrane proteins execute significant roles in cellular processes of living organisms, ranging from cell signaling to cell adhesion. As a major part of a cell, the identification of membrane proteins and their functional types become a challenging jo...
IEEE/ACM transactions on computational biology and bioinformatics
Jan 5, 2018
As one of the most challenging tasks in sequence analysis, protein remote homology detection has been extensively studied. Methods based on discriminative models and ranking approaches have achieved the state-of-the-art performance, and these two kin...
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