AIMC Topic: Sequence Alignment

Clear Filters Showing 11 to 20 of 144 articles

Protein function annotation and virulence factor identification of Klebsiella pneumoniae genome by multiple machine learning models.

Microbial pathogenesis Jun 6, 2024
Klebsiella pneumoniae is a type of Gram-negative bacterium which can cause a range of infections in human. In recent years, an increasing number of strains of K. pneumoniae resistant to multiple antibiotics have emerged, posing a significant threat t...
Proteome Klebsiella Infections Klebsiella pneumoniae Computational Biology Molecular Sequence Annotation Humans Genome, Bacterial Machine Learning Sequence Alignment Bacterial Proteins Virulence Factors
View on PubMed DOI

Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data.

Nature methods Jan 2, 2024
Leveraging iterative alignment search through genomic and metagenome sequence databases, we report the DeepMSA2 pipeline for uniform protein single- and multichain multiple-sequence alignment (MSA) construction. Large-scale benchmarks show that DeepM...
Proteins Sequence Alignment Genomics Computational Biology Algorithms Deep Learning
View on PubMed DOI

AttCON: With better MSAs and attention mechanism for accurate protein contact map prediction.

Computers in biology and medicine Dec 5, 2023
Protein contact map prediction is a critical and vital step in protein structure prediction, and its accuracy is highly contingent upon the feature representations of protein sequence information and the efficacy of deep learning models. In this pape...
Neural Networks, Computer Proteins Sequence Alignment Algorithms Computational Biology
View on PubMed DOI

Predicting multiple conformations via sequence clustering and AlphaFold2.

Nature Nov 13, 2023
AlphaFold2 (ref. ) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends on multiple conformational substates, and disease-causing point mutations often ca...
Rhodobacter sphaeroides Protein Folding Sequence Alignment Proteins Bacterial Proteins Mutation Protein Conformation Machine Learning Cluster Analysis
View on PubMed DOI

Protein remote homology detection and structural alignment using deep learning.

Nature biotechnology Sep 7, 2023
Exploiting sequence-structure-function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec...
Sequence Alignment Sequence Analysis, Protein Deep Learning Computational Biology Databases, Protein Algorithms Protein Conformation Proteins
View on PubMed DOI

Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15.

Proteins Aug 31, 2023
We report the results of the "UM-TBM" and "Zheng" groups in CASP15 for protein monomer and complex structure prediction. These prediction sets were obtained using the D-I-TASSER and DMFold-Multimer algorithms, respectively. For monomer structure pred...
Protein Conformation Sequence Alignment Proteins Models, Molecular Algorithms Software Deep Learning
View on PubMed DOI

ModelRevelator: Fast phylogenetic model estimation via deep learning.

Molecular phylogenetics and evolution Aug 16, 2023
Selecting the best model of sequence evolution for a multiple-sequence-alignment (MSA) constitutes the first step of phylogenetic tree reconstruction. Common approaches for inferring nucleotide models typically apply maximum likelihood (ML) methods, ...
Phylogeny Deep Learning Sequence Alignment Nucleotides Likelihood Functions
View on PubMed DOI

AiKPro: deep learning model for kinome-wide bioactivity profiling using structure-based sequence alignments and molecular 3D conformer ensemble descriptors.

Scientific reports Jun 24, 2023
The discovery of selective and potent kinase inhibitors is crucial for the treatment of various diseases, but the process is challenging due to the high structural similarity among kinases. Efficient kinome-wide bioactivity profiling is essential for...
Eye, Artificial Drug Design Protein Kinase Inhibitors Deep Learning Sequence Alignment Ligands
View on PubMed DOI

Machine learning methods for predicting protein structure from single sequences.

Current opinion in structural biology Jun 13, 2023
Recent breakthroughs in protein structure prediction have increasingly relied on the use of deep neural networks. These recent methods are notable in that they produce 3-D atomic coordinates as a direct output of the networks, a feature which present...
Neural Networks, Computer Sequence Alignment Machine Learning Proteins
View on PubMed DOI

Deep reinforcement learning-based pairwise DNA sequence alignment method compatible with embedded edge devices.

Scientific reports Feb 16, 2023
Sequence alignment is an essential component of bioinformatics, for identifying regions of similarity that may indicate functional, structural, or evolutionary relationships between the sequences. Genome-based diagnostics relying on DNA sequencing ha...
Sequence Alignment Neural Networks, Computer Computers Algorithms DNA
View on PubMed DOI
Popular Topics
Recent Journals