AIMC Topic: Sequence Alignment

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Identification of the tail assembly chaperone genes of T4-Like phages suggests a mechanism other than translational frameshifting for biogenesis of their encoded proteins.

Virology Nov 18, 2021
Tape measure (TM) proteins are essential for the formation of long-tailed phages. TM protein assembly into tails requires the action of tail assembly chaperones (TACs). TACs (e.g. gpG and gpT of E. coli phage lambda) are usually produced in a short (...
Virus Assembly Sequence Alignment Sequence Homology, Amino Acid Viral Tail Proteins Bacteriophage T4 Escherichia coli Virion Amino Acid Sequence Genome, Viral Conserved Sequence Bacteria Frameshifting, Ribosomal Computational Biology Molecular Chaperones
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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 Conserved Sequence Sequence Analysis, Protein Deep Learning Bacterial Proteins Evolution, Molecular Metagenomics RNA, Ribosomal Archaeal Proteins
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PIC-Me: paralogs and isoforms classifier based on machine-learning approaches.

BMC bioinformatics Oct 21, 2021
BACKGROUND: Paralogs formed through gene duplication and isoforms formed through alternative splicing have been important processes for increasing protein diversity and maintaining cellular homeostasis. Despite their recognized importance and the adv...
Protein Isoforms Sequence Alignment Alternative Splicing Machine Learning Molecular Sequence Annotation
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Mapping the glycosyltransferase fold landscape using interpretable deep learning.

Nature communications Sep 27, 2021
Glycosyltransferases (GTs) play fundamental roles in nearly all cellular processes through the biosynthesis of complex carbohydrates and glycosylation of diverse protein and small molecule substrates. The extensive structural and functional diversifi...
Deep Learning Computational Biology Glycosylation Protein Structure, Secondary Protein Folding Sequence Alignment Databases, Genetic Amino Acid Sequence Datasets as Topic Protein Structure, Tertiary Glycosyltransferases
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Development and validation of multiple machine learning algorithms for the classification of G-protein-coupled receptors using molecular evolution model-based feature extraction strategy.

Amino acids Sep 25, 2021
Machine learning is one of the most potential ways to realize the function prediction of the incremental large-scale G-protein-coupled receptors (GPCR). Prior research reveals that the key to determining the overall classification accuracy of GPCR is...
Receptors, G-Protein-Coupled Amino Acid Sequence Multigene Family Sequence Alignment Machine Learning Algorithms Evolution, Molecular
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Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14.

Proteins Aug 19, 2021
This article reports and analyzes the results of protein contact and distance prediction by our methods in the 14th Critical Assessment of techniques for protein Structure Prediction (CASP14). A new deep learning-based contact/distance predictor was ...
Sequence Alignment Sequence Analysis, Protein Models, Molecular Protein Conformation Software Deep Learning Computational Biology Proteins
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Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14.

Proteins Aug 7, 2021
In this article, we report 3D structure prediction results by two of our best server groups ("Zhang-Server" and "QUARK") in CASP14. These two servers were built based on the D-I-TASSER and D-QUARK algorithms, which integrated four newly developed com...
Protein Folding Sequence Alignment Sequence Analysis, Protein Deep Learning Computational Biology Proteins Models, Molecular Protein Conformation Hydrogen Bonding Software
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Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14.

Proteins Jul 27, 2021
Substantial progresses in protein structure prediction have been made by utilizing deep-learning and residue-residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by inc...
Sequence Alignment Protein Structure, Tertiary Sequence Analysis, Protein Deep Learning Humans Proteins Models, Molecular Software Algorithms
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Highly accurate protein structure prediction with AlphaFold.

Nature Jul 15, 2021
Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort, the structures of around 100,000 unique proteins have been determined, but this r...
Neural Networks, Computer Reproducibility of Results Deep Learning Protein Folding Models, Molecular Computational Biology Amino Acid Sequence Sequence Alignment Proteins Protein Conformation Databases, Protein
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MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction.

Scientific reports Jun 23, 2021
Protein structure prediction is an important problem in bioinformatics and has been studied for decades. However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field. In this paper, we p...
Software Sequence Alignment Protein Structure, Tertiary Deep Learning Structure-Activity Relationship Models, Molecular Amino Acid Sequence
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