While a plethora of different protein-ligand docking protocols have been developed over the past twenty years, their performances greatly depend on the provided input protein-ligand pair. In this study, we developed a machine-learning model that uses...
Protein phosphorylation is essential for regulating cellular activities by modifying substrates at specific residues, which frequently interact with proteins containing phosphoprotein-binding domains (PPBDs) to propagate the phosphorylation signaling...
Top-down mass spectrometry has become the main method for intact proteoform identification, characterization, and quantitation. Because of the complexity of top-down mass spectrometry data, spectral deconvolution is an indispensable step in spectral ...
Protein secondary structure prediction remains a vital topic with broad applications. Due to lack of a widely accepted standard in secondary structure predictor evaluation, a fair comparison of predictors is challenging. A detailed examination of fac...
Journal of bioinformatics and computational biology
May 5, 2020
Presynaptic and postsynaptic neurotoxins are two types of neurotoxins from venomous animals and functionally important molecules in the neurosciences; however, their experimental characterization is difficult, time-consuming, and costly. Therefore, b...
Many proteins exist in natures as oligomers with various quaternary structural attributes rather than as single chains. Predicting these attributes is an essential task in computational biology for the advancement of proteomics. However, the existing...
The three-dimensional structures populated by a protein molecule determine to a great extent its biological activities. The rich information encoded by protein structure on protein function continues to motivate the development of computational appro...
Antibodies are capable of potently and specifically binding individual antigens and, in some cases, disrupting their functions. The key challenge in generating antibody-based inhibitors is the lack of fundamental information relating sequences of ant...
A massive number of biological entities, such as genes and mutations, are mentioned in the biomedical literature. The capturing of the semantic relatedness of biological entities is vital to many biological applications, such as protein-protein inter...
DNA-binding proteins (DBPs) play vital roles in all aspects of genetic activities. However, the identification of DBPs by using wet-lab experimental approaches is often time-consuming and laborious. In this study, we develop a novel computational met...
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