AIMC Topic: Sequence Analysis, Protein

Clear Filters Showing 41 to 50 of 262 articles

Improved Protein Structure Prediction Using a New Multi-Scale Network and Homologous Templates.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Oct 31, 2021
The accuracy of de novo protein structure prediction has been improved considerably in recent years, mostly due to the introduction of deep learning techniques. In this work, trRosettaX, an improved version of trRosetta for protein structure predicti...
Protein Conformation Sequence Analysis, Protein Neural Networks, Computer Deep Learning Computational Biology Models, Molecular Datasets as Topic
View on PubMed DOI

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 ...
Deep Learning Evolution, Molecular Bacterial Proteins Conserved Sequence Sequence Analysis, Protein Metagenomics Archaeal Proteins RNA, Ribosomal Sequence Alignment
View on PubMed DOI

Protein Family Classification from Scratch: A CNN Based Deep Learning Approach.

IEEE/ACM transactions on computational biology and bioinformatics Oct 8, 2021
Next-generation sequencing techniques provide us with an opportunity for generating sequenced proteins and identifying the biological families and functions of these proteins. However, compared with identified proteins, uncharacterized proteins consi...
Algorithms Deep Learning Computational Biology Humans Sequence Analysis, Protein Cluster Analysis Proteins Amino Acid Sequence
View on PubMed DOI

Multi-Scale Capsule Network for Predicting DNA-Protein Binding Sites.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2021
Discovering DNA-protein binding sites, also known as motif discovery, is the foundation for further analysis of transcription factors (TFs). Deep learning algorithms such as convolutional neural networks (CNN) have been introduced to motif discovery ...
Sequence Analysis, Protein Chromatin Immunoprecipitation Sequencing Deep Learning Algorithms Protein Binding Computational Biology Transcription Factors DNA-Binding Proteins Binding Sites
View on PubMed DOI

AIEpred: An Ensemble Predictive Model of Classifier Chain to Identify Anti-Inflammatory Peptides.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2021
Anti-inflammatory peptides (AIEs) have recently emerged as promising therapeutic agent for treatment of various inflammatory diseases, such as rheumatoid arthritis and Alzheimer's disease. Therefore, detecting the correlation between amino acid seque...
Sequence Analysis, Protein Drug Discovery Computational Biology Models, Statistical Anti-Inflammatory Agents Amino Acid Sequence Machine Learning Algorithms Peptides
View on PubMed DOI

Protein Fold Recognition by Combining Support Vector Machines and Pairwise Sequence Similarity Scores.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2021
Protein fold recognition is one of the most essential steps for protein structure prediction, aiming to classify proteins into known protein folds. There are two main computational approaches: one is the template-based method based on the alignment s...
Algorithms Computational Biology Pattern Recognition, Automated Support Vector Machine Protein Folding Proteins Sequence Analysis, Protein
View on PubMed DOI

When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14-(tFold for CASP14 contact prediction).

Proteins Sep 23, 2021
In this paper, we report our tFold framework's performance on the inter-residue contact prediction task in the 14th Critical Assessment of protein Structure Prediction (CASP14). Our tFold framework seamlessly combines both homologous sequences and st...
Neural Networks, Computer Software Reproducibility of Results Computational Biology Proteins Sequence Analysis, Protein Models, Molecular Structural Homology, Protein Protein Folding
View on PubMed DOI

PARROT is a flexible recurrent neural network framework for analysis of large protein datasets.

eLife Sep 17, 2021
The rise of high-throughput experiments has transformed how scientists approach biological questions. The ubiquity of large-scale assays that can test thousands of samples in a day has necessitated the development of new computational approaches to i...
Phosphorylation Software High-Throughput Nucleotide Sequencing Humans Deep Learning Sequence Analysis, Protein Proteins Computational Biology Neural Networks, Computer Databases, Protein
View on PubMed DOI

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 ...
Protein Conformation Software Sequence Analysis, Protein Sequence Alignment Computational Biology Deep Learning Proteins Models, Molecular
View on PubMed DOI

Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14.

Proteins Aug 17, 2021
The trRosetta structure prediction method employs deep learning to generate predicted residue-residue distance and orientation distributions from which 3D models are built. We sought to improve the method by incorporating as inputs (in addition to se...
Proteins Protein Structure, Tertiary Humans Sequence Analysis, Protein Metagenome Deep Learning Software Computational Biology
View on PubMed DOI
Popular Topics
Recent Journals