AIMC Topic: Sequence Alignment

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AMPGen: an evolutionary information-reserved and diffusion-driven generative model for de novo design of antimicrobial peptides.

Communications biology May 30, 2025
The rapid advancement of artificial intelligence (AI) has enabled de novo design of functional proteins, circumventing the reliance on natural templates or sequencing databases. However, current protein design models are ineffective in generating pro...
Evolution, Molecular Sequence Alignment Antimicrobial Peptides Anti-Bacterial Agents Drug Design Artificial Intelligence Software
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ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction.

IEEE transactions on neural networks and learning systems May 2, 2025
Protein function prediction is crucial for understanding species evolution, including viral mutations. Gene ontology (GO) is a standardized representation framework for describing protein functions with annotated terms. Each ontology is a specific fu...
Algorithms Deep Learning Computational Biology Humans Neural Networks, Computer Molecular Sequence Annotation Gene Ontology Sequence Alignment Proteins Databases, Protein
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TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning.

Communications biology Apr 5, 2025
Identifying DNA-binding proteins and their binding residues is critical for understanding diverse biological processes, but conventional experimental approaches are slow and costly. Existing machine learning methods, while faster, often lack accuracy...
Deep Learning Computational Biology Sequence Alignment Sequence Analysis, Protein DNA-Binding Proteins Humans Software
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Simpler Protein Domain Identification Using Spectral Clustering.

Proteins Feb 13, 2025
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
Proteins Databases, Protein Algorithms Protein Conformation Models, Molecular Computational Biology Deep Learning Sequence Alignment Protein Domains Cluster Analysis Sequence Analysis, Protein Amino Acid Sequence
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Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.

PLoS computational biology Dec 30, 2024
The 3D structure of RNA critically influences its functionality, and understanding this structure is vital for deciphering RNA biology. Experimental methods for determining RNA structures are labour-intensive, expensive, and time-consuming. Computati...
Nucleic Acid Conformation Sequence Alignment Deep Learning Computational Biology Benchmarking RNA Sequence Analysis, RNA
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Splam: a deep-learning-based splice site predictor that improves spliced alignments.

Genome biology Sep 16, 2024
The process of splicing messenger RNA to remove introns plays a central role in creating genes and gene variants. We describe Splam, a novel method for predicting splice junctions in DNA using deep residual convolutional neural networks. Unlike previ...
Humans Neural Networks, Computer Sequence Alignment RNA Splicing Deep Learning RNA Splice Sites Introns
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Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments.

Molecular phylogenetics and evolution Aug 30, 2024
Phylogenetic tree reconstruction with molecular data is important in many fields of life science research. The gold standard in this discipline is the phylogenetic tree reconstruction based on the Maximum Likelihood method. In this study, we present ...
Sequence Alignment Evolution, Molecular Likelihood Functions Neural Networks, Computer Machine Learning Phylogeny Models, Genetic
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Using AlphaFold Multimer to discover interkingdom protein-protein interactions.

The Plant journal : for cell and molecular biology Aug 17, 2024
Structural prediction by artificial intelligence can be powerful new instruments to discover novel protein-protein interactions, but the community still grapples with the implementation, opportunities and limitations. Here, we discuss and re-analyse ...
Artificial Intelligence Protein Interaction Mapping Plant Proteins Sequence Alignment
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Reliable estimation of tree branch lengths using deep neural networks.

PLoS computational biology Aug 5, 2024
A phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the t...
Evolution, Molecular Likelihood Functions Neural Networks, Computer Sequence Alignment Machine Learning Phylogeny Computational Biology Algorithms Deep Learning Models, Genetic
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SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models.

Genome biology Jul 25, 2024
Accurate inference of orthologous genes constitutes a prerequisite for comparative and evolutionary genomics. SonicParanoid is one of the fastest tools for orthology inference; however, its scalability and accuracy have been hampered by time-consumin...
Humans Machine Learning Software Genomics Sequence Alignment
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