AIMC Topic: Evolution, Molecular

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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...
Computational Biology Databases, Protein Support Vector Machine Evolution, Molecular DNA-Binding Proteins
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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...
Evolution, Molecular Humans Influenza, Human Influenza Vaccines Machine Learning Phylogeny
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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 ...
Intrinsically Disordered Proteins Deep Learning Evolution, Molecular Internet Amino Acid Sequence Computational Biology
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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...
Protein Interaction Mapping Machine Learning Databases, Protein Humans Saccharomyces cerevisiae Proteins Sequence Analysis, Protein Computational Biology Evolution, Molecular Proteins Helicobacter pylori Amino Acid Sequence Animals Protein Interaction Maps
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Prediction of essential genes in prokaryote based on artificial neural network.

Genes & genomics Nov 17, 2019
BACKGROUND: Rapid identification of new essential genes is necessary to understand biological mechanisms and identify potential targets for antimicrobial drugs. Many computational methods have been proposed.
Neural Networks, Computer Algorithms Predictive Value of Tests Genes, Essential Bacteria Computational Biology Bacterial Proteins Evolution, Molecular
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PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution.

BMC genomics Jul 12, 2019
BACKGROUND: Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequences of diploid progenitors. In...
Repetitive Sequences, Nucleic Acid Phylogeny Genome, Plant DNA, Plant Polyploidy Genomics Evolution, Molecular Unsupervised Machine Learning Triticum Nicotiana
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Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites.

Proteins Jun 22, 2019
Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity or regulatory binding sites (allosteric sites), that modulate the activity of functional binding sites throu...
Binding Sites Databases, Protein Artificial Intelligence Machine Learning Humans Algorithms Protein Binding Allosteric Site Evolution, Molecular Allosteric Regulation Proteins Molecular Dynamics Simulation Protein Conformation
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DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information.

Journal of computer-aided molecular design May 23, 2019
DNA-binding proteins (DBPs) participate in various biological processes including DNA replication, recombination, and repair. In the human genome, about 6-7% of these proteins are utilized for genes encoding. DBPs shape the DNA into a compact structu...
Humans Binding Sites Animals Position-Specific Scoring Matrices Support Vector Machine Databases, Protein Evolution, Molecular DNA DNA-Binding Proteins Machine Learning Algorithms
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Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction.

EBioMedicine Apr 29, 2019
BACKGROUND: The diagnosis of multidrug resistant and extensively drug resistant tuberculosis is a global health priority. Whole genome sequencing of clinical Mycobacterium tuberculosis isolates promises to circumvent the long wait times and limited s...
Extensively Drug-Resistant Tuberculosis Databases, Genetic Cluster Analysis Models, Statistical Genetic Variation Humans Mycobacterium tuberculosis ROC Curve Genome, Bacterial Evolution, Molecular Genomics Machine Learning Antitubercular Agents Computational Biology Tuberculosis, Multidrug-Resistant Prognosis Reproducibility of Results Microbial Sensitivity Tests
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End-to-End Differentiable Learning of Protein Structure.

Cell systems Apr 17, 2019
Predicting protein structure from sequence is a central challenge of biochemistry. Co-evolution methods show promise, but an explicit sequence-to-structure map remains elusive. Advances in deep learning that replace complex, human-designed pipelines ...
Evolution, Molecular Protein Folding Sequence Analysis, Protein Machine Learning Software
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