AIMC Topic: Evolution, Molecular

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Deep learning-powered enzyme efficiency boosting with evolutionary information.

Science bulletin Mar 19, 2024
Deep Learning Evolution, Molecular Enzymes
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The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations.

Journal of computer-aided molecular design Mar 19, 2024
Computer-aided drug design has advanced rapidly in recent years, and multiple instances of in silico designed molecules advancing to the clinic have demonstrated the contribution of this field to medicine. Properly designed and implemented platforms ...
Algorithms Drug Design Evolution, Molecular Artificial Intelligence
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Evolutionary-scale prediction of atomic-level protein structure with a language model.

Science (New York, N.Y.) Mar 16, 2023
Recent advances in machine learning have leveraged evolutionary information in multiple sequence alignments to predict protein structure. We demonstrate direct inference of full atomic-level protein structure from primary sequence using a large langu...
Protein Conformation Sequence Analysis, Protein Evolution, Molecular Proteins Machine Learning Amino Acid Sequence
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Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning.

Nature communications Aug 17, 2022
A neutral network connects all genotypes with equivalent phenotypes in a fitness landscape and plays an important role in the mutational robustness and evolvability of biomolecules. In contrast to earlier theoretical works, evidence of large neutral ...
Models, Genetic Algorithms Evolution, Molecular Deep Learning Genetic Fitness Mutation Genotype RNA, Catalytic
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Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography.

BMC genomics May 7, 2022
BACKGROUND: We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5,...
Humans Phylogeny Bayes Theorem DNA, Mitochondrial Haplotypes Europe Evolution, Molecular Unsupervised Machine Learning Phylogeography Genetics, Population
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Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling.

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...
Classification Evolution, Molecular Amino Acid Sequence Neural Networks, Computer Computer Simulation Phylogeny Deep Learning Computational Biology Databases, Genetic
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Computed structures of core eukaryotic protein complexes.

Science (New York, N.Y.) Dec 10, 2021
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...
Homologous Recombination Chromosome Segregation Ligases Multiprotein Complexes Acyltransferases Computer Simulation Deep Learning Protein Interaction Maps Computational Biology Proteome Ubiquitin Protein Interaction Mapping Saccharomyces cerevisiae Proteins DNA Repair Protein Biosynthesis Ribosomes Models, Molecular Protein Conformation Saccharomyces cerevisiae Membrane Proteins Evolution, Molecular
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Co-evolution based machine-learning for predicting functional interactions between human genes.

Nature communications Nov 9, 2021
Over the next decade, more than a million eukaryotic species are expected to be fully sequenced. This has the potential to improve our understanding of genotype and phenotype crosstalk, gene function and interactions, and answer evolutionary question...
DNA Repair Phylogeny Sequence Analysis, DNA Evolution, Molecular Humans Machine Learning
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TwinCons: Conservation score for uncovering deep sequence similarity and divergence.

PLoS computational biology Oct 29, 2021
We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a 'cost' of transforming one ...
Sequence Alignment Archaeal Proteins Conserved Sequence Bacterial Proteins Sequence Analysis, Protein Deep Learning Metagenomics Evolution, Molecular RNA, Ribosomal
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Disease variant prediction with deep generative models of evolutionary data.

Nature Oct 27, 2021
Quantifying the pathogenicity of protein variants in human disease-related genes would have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of these variants still have unknown consequences. In principle, computational...
Proteins Unsupervised Machine Learning Models, Molecular Genetic Predisposition to Disease Evolution, Molecular Disease Selection, Genetic Genetic Fitness Bayes Theorem Biological Assay Genetic Variation Humans Phenotype
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