In biological systems, Glutamic acid is a crucial amino acid which is used in protein biosynthesis. Carboxylation of glutamic acid is a significant post-translational modification which plays important role in blood coagulation by activating prothrom...
Journal of computational biology : a journal of computational molecular cell biology
Jan 5, 2022
Deep neural networks (DNNs) have been recently proposed for quartet tree phylogeny estimation. Here, we present a study evaluating recently trained DNNs in comparison to a collection of standard phylogeny estimation methods on a heterogeneous collect...
International journal of molecular sciences
Dec 17, 2021
Protein solubility is an important thermodynamic parameter that is critical for the characterization of a protein's function, and a key determinant for the production yield of a protein in both the research setting and within industrial (e.g., pharma...
Machine-learning models that learn from data to predict how protein sequence encodes function are emerging as a useful protein engineering tool. However, when using these models to suggest new protein designs, one must deal with the vast combinatoria...
Although advancing the therapeutic alternatives for treating deadly cancers has gained much attention globally, still the primary methods such as chemotherapy have significant downsides and low specificity. Most recently, Anticancer peptides (ACPs) h...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2021
Protein fold recognition is critical for studies of the protein structure prediction and drug design. Several methods have been proposed to obtain discriminative features from the protein sequences for fold recognition. However, the ensemble methods ...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2021
Protein Secondary Structural Class (PSSC) information is important in investigating further challenges of protein sequences like protein fold recognition, protein tertiary structure prediction, and analysis of protein functions for drug discovery. Id...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2021
The discovery of potential Drug-Target Interactions (DTIs) is a determining step in the drug discovery and repositioning process, as the effectiveness of the currently available antibiotic treatment is declining. Although putting efforts on the tradi...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2021
Knowledge of protein functions plays an important role in biology and medicine. With the rapid development of high-throughput technologies, a huge number of proteins have been discovered. However, there are a great number of proteins without function...
There has been considerable recent progress in protein structure prediction using deep neural networks to predict inter-residue distances from amino acid sequences. Here we investigate whether the information captured by such networks is sufficiently...
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