AIMC Topic: Sequence Alignment

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Condition-Invariant Robot Localization Using Global Sequence Alignment of Deep Features.

Sensors (Basel, Switzerland) Jun 15, 2021
Localization is one of the essential process in robotics, as it plays an important role in autonomous navigation, simultaneous localization, and mapping for mobile robots. As robots perform large-scale and long-term operations, identifying the same l...
Sequence Alignment Algorithms Robotics Motion
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Recent Applications of Deep Learning Methods on Evolution- and Contact-Based Protein Structure Prediction.

International journal of molecular sciences Jun 2, 2021
The new advances in deep learning methods have influenced many aspects of scientific research, including the study of the protein system. The prediction of proteins' 3D structural components is now heavily dependent on machine learning techniques tha...
Machine Learning Software Deep Learning Amino Acid Sequence Computational Biology Humans Protein Conformation Evolution, Molecular Neural Networks, Computer Sequence Alignment Databases, Protein
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CopulaNet: Learning residue co-evolution directly from multiple sequence alignment for protein structure prediction.

Nature communications May 5, 2021
Residue co-evolution has become the primary principle for estimating inter-residue distances of a protein, which are crucially important for predicting protein structure. Most existing approaches adopt an indirect strategy, i.e., inferring residue co...
Humans Neural Networks, Computer Caspases Sequence Alignment Protein Structure, Tertiary Proteins Models, Molecular Mutation Machine Learning Computational Biology
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Analyzing effect of quadruple multiple sequence alignments on deep learning based protein inter-residue distance prediction.

Scientific reports Apr 7, 2021
Protein 3D structure prediction has advanced significantly in recent years due to improving contact prediction accuracy. This improvement has been largely due to deep learning approaches that predict inter-residue contacts and, more recently, distanc...
Proteins Models, Molecular Caspases Neural Networks, Computer Deep Learning Protein Interaction Domains and Motifs Sequence Alignment Protein Structure, Tertiary Sequence Analysis, Protein
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Trivial and nontrivial error sources account for misidentification of protein partners in mutual information approaches.

Scientific reports Mar 25, 2021
The problem of finding the correct set of partners for a given pair of interacting protein families based on multi-sequence alignments (MSAs) has received great attention over the years. Recently, the native contacts of two interacting proteins were ...
Machine Learning Models, Genetic Sequence Alignment Evolution, Molecular Biological Coevolution Proteins
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MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization.

Journal of chemical information and modeling Mar 23, 2021
Small molecules play a critical role in modulating biological systems. Knowledge of chemical-protein interactions helps address fundamental and practical questions in biology and medicine. However, with the rapid emergence of newly sequenced genes, t...
Machine Learning Phylogeny Humans Computational Biology Amino Acid Sequence Ligands Sequence Alignment
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2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.

Genome biology Mar 1, 2021
Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the true complexity of processing. However, the relatively high error rates of long-read sequencing technolog...
Computational Biology Molecular Sequence Annotation Introns Sequence Alignment RNA Splicing RNA Splice Sites Algorithms Reproducibility of Results RNA-Seq Machine Learning Software
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Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Bagging Multiple Sequence Alignment Learning.

Journal of computational biology : a journal of computational molecular cell biology Feb 22, 2021
Protein Conformation Protein Structure, Secondary Sequence Alignment Computational Biology Proteins Position-Specific Scoring Matrices Neural Networks, Computer Algorithms Deep Learning
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Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction.

Proteins Feb 16, 2021
Deep learning has emerged as a revolutionary technology for protein residue-residue contact prediction since the 2012 CASP10 competition. Considerable advancements in the predictive power of the deep learning-based contact predictions have been achie...
Binding Sites Sequence Alignment Sequence Analysis, Protein Protein Interaction Domains and Motifs Databases, Protein Benchmarking Protein Conformation Computational Biology Proteins Research Design Deep Learning Protein Binding Humans Software
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Protein2Vec: Aligning Multiple PPI Networks with Representation Learning.

IEEE/ACM transactions on computational biology and bioinformatics Feb 3, 2021
Research of Protein-Protein Interaction (PPI) Network Alignment is playing an important role in understanding the crucial underlying biological knowledge such as functionally homologous proteins and conserved evolutionary pathways across different sp...
Computational Biology Protein Interaction Mapping Sequence Alignment Algorithms Humans Animals Machine Learning Protein Interaction Maps
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