AIMC Topic: Evolution, Molecular
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Inter-protein residue covariation information unravels physically interacting protein dimers.
BMC bioinformatics
Dec 17, 2020
BACKGROUND: Predicting physical interaction between proteins is one of the greatest challenges in computational biology. There are considerable various protein interactions and a huge number of protein sequences and synthetic peptides with unknown in...
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure.
Nature communications
Dec 1, 2020
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression leve...
Evolutionary insights into the active-site structures of the metallo-β-lactamase superfamily from a classification study with support vector machine.
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry
Sep 18, 2020
The metallo-β-lactamase (MβL) superfamily, which is intriguing due to its enzyme promiscuity, is a good model enzyme superfamily for studies of catalytic function evolution. Our previous study traced the evolution of the phosphotriesterase activity o...
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.
Open biology
Sep 2, 2020
Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionall...
A novel fusion based on the evolutionary features for protein fold recognition using support vector machines.
Scientific reports
Sep 1, 2020
Protein fold recognition plays a crucial role in discovering three-dimensional structure of proteins and protein functions. Several approaches have been employed for the prediction of protein folds. Some of these approaches are based on extracting fe...
Genes, the brain, and artificial intelligence in evolution.
Journal of human genetics
Jul 27, 2020
Three important systems, genes, the brain, and artificial intelligence (especially deep learning) have similar goals, namely, the maximization of likelihood or minimization of cross-entropy. Animal brains have evolved through predator-prey interactio...
Use Chou's 5-Step Rule to Predict DNA-Binding Proteins with Evolutionary Information.
BioMed research international
Jul 27, 2020
The knowledge of DNA-binding proteins would help to understand the functions of proteins better in cellular biological processes. Research on the prediction of DNA-binding proteins can promote the research of drug proteins and computer acidified drug...
Predicting the short-term success of human influenza virus variants with machine learning.
Proceedings. Biological sciences
Apr 8, 2020
Seasonal influenza viruses are constantly changing and produce a different set of circulating strains each season. Small genetic changes can accumulate over time and result in antigenically different viruses; this may prevent the body's immune system...
SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning.
Genomics, proteomics & bioinformatics
Mar 13, 2020
Intrinsically disordered or unstructured proteins (or regions in proteins) have been found to be important in a wide range of biological functions and implicated in many diseases. Due to the high cost and low efficiency of experimental determination ...
Using Weighted Extreme Learning Machine Combined With Scale-Invariant Feature Transform to Predict Protein-Protein Interactions From Protein Evolutionary Information.
IEEE/ACM transactions on computational biology and bioinformatics
Jan 10, 2020
Protein-Protein Interactions (PPIs) play an irreplaceable role in biological activities of organisms. Although many high-throughput methods are used to identify PPIs from different kinds of organisms, they have some shortcomings, such as high cost an...
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