BACKGROUND: Families of related proteins and their different functions may be described systematically using common classifications and ontologies such as Pfam and GO (Gene Ontology), for example. However, many proteins consist of multiple domains, a...
BACKGROUND: Determining protein-protein interactions and their binding affinity are important in understanding cellular biological processes, discovery and design of novel therapeutics, protein engineering, and mutagenesis studies. Due to the time an...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 9, 2018
Protein tertiary structure prediction is an important open challenge in bioinformatics and requires effective methods to accurately evaluate the quality of protein 3-D models generated computationally. Many quality assessment (QA) methods have been p...
Protein gamma-turn prediction is useful in protein function studies and experimental design. Several methods for gamma-turn prediction have been developed, but the results were unsatisfactory with Matthew correlation coefficients (MCC) around 0.2-0.4...
Understanding the function of human proteins is essential to decipher the molecular mechanisms of human diseases and phenotypes. Of the 17 470 human protein coding genes in the neXtProt 2018-01-17 database with unequivocal protein existence evidence ...
Journal of chemical information and modeling
Oct 16, 2018
Machine learning has shown enormous potential for computer-aided drug discovery. Here we show how modern convolutional neural networks (CNNs) can be applied to structure-based virtual screening. We have coupled our densely connected CNN (DenseNet) wi...
Predicting protein structure from sequence alone is challenging. Thus, the majority of methods for protein structure prediction rely on evolutionary information from multiple sequence alignments. In previous work we showed that Long Short-Term Bidire...
Journal of chemical theory and computation
Oct 9, 2018
The value of protein models obtained with automated protein structure prediction depends primarily on their accuracy. Protein model quality assessment is thus critical to select the model that can best answer biologically relevant questions from an e...
Protein nitration and nitrosylation are essential post-translational modifications (PTMs) involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are...
BACKGROUND: The ability to predict the interaction of drugs with target proteins is essential to research and development of drug. However, the traditional experimental paradigm is costly, and previous in silico prediction paradigms have been impeded...
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