AIMC Topic: Sequence Analysis, Protein

Clear Filters Showing 51 to 60 of 262 articles

PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction.

International journal of molecular sciences Aug 17, 2021
Protein Blocks (PBs) are a widely used structural alphabet describing local protein backbone conformation in terms of 16 possible conformational states, adopted by five consecutive amino acids. The representation of complex protein 3D structures as 1...
Models, Molecular Protein Conformation Sequence Analysis, Protein Neural Networks, Computer Software Algorithms Deep Learning Humans Proteins Databases, Protein
View on PubMed DOI

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

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...
Software Algorithms Deep Learning Humans Protein Structure, Tertiary Proteins Sequence Analysis, Protein Models, Molecular Sequence Alignment
View on PubMed DOI

A Deep-Learning Sequence-Based Method to Predict Protein Stability Changes Upon Genetic Variations.

Genes Jun 12, 2021
Several studies have linked disruptions of protein stability and its normal functions to disease. Therefore, during the last few decades, many tools have been developed to predict the free energy changes upon protein residue variations. Most of these...
Molecular Dynamics Simulation Genetic Variation Protein Stability Humans Deep Learning Amino Acid Substitution Sequence Analysis, Protein
View on PubMed DOI

MILAMP: Multiple Instance Prediction of Amyloid Proteins.

IEEE/ACM transactions on computational biology and bioinformatics Jun 3, 2021
Amyloid proteins are implicated in several diseases such as Parkinson's, Alzheimer's, prion diseases, etc. In order to characterize the amyloidogenicity of a given protein, it is important to locate the amyloid forming hotspot regions within the prot...
Amyloidogenic Proteins Humans Machine Learning Computational Biology Databases, Protein Sequence Analysis, Protein
View on PubMed DOI

Deep Learning-Based Advances in Protein Structure Prediction.

International journal of molecular sciences May 24, 2021
Obtaining an accurate description of protein structure is a fundamental step toward understanding the underpinning of biology. Although recent advances in experimental approaches have greatly enhanced our capabilities to experimentally determine prot...
Sequence Analysis, Protein Amino Acid Sequence Protein Conformation Cryoelectron Microscopy Proteins Databases, Protein Models, Molecular Neural Networks, Computer Software Algorithms Deep Learning Computational Biology
View on PubMed DOI

Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning.

Nature biomedical engineering Apr 15, 2021
The optimization of therapeutic antibodies is time-intensive and resource-demanding, largely because of the low-throughput screening of full-length antibodies (approximately 1 × 10 variants) expressed in mammalian cells, which typically results in fe...
Receptor, ErbB-2 Antibody Affinity Humans Trastuzumab Animals Antigens Sequence Analysis, Protein CRISPR-Cas Systems Hybridomas Recombinational DNA Repair Amino Acid Sequence Deep Learning Mutagenesis, Site-Directed Antibody Specificity Protein Binding Protein Engineering
View on PubMed DOI

The whole is greater than its parts: ensembling improves protein contact prediction.

Scientific reports Apr 13, 2021
The prediction of amino acid contacts from protein sequence is an important problem, as protein contacts are a vital step towards the prediction of folded protein structures. We propose that a powerful concept from deep learning, called ensembling, c...
Models, Molecular Protein Conformation Protein Folding Sequence Analysis, Protein Deep Learning Computational Biology Proteins Neural Networks, Computer Software Algorithms
View on PubMed DOI

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...
Neural Networks, Computer Deep Learning Protein Interaction Domains and Motifs Proteins Sequence Alignment Models, Molecular Protein Structure, Tertiary Caspases Sequence Analysis, Protein
View on PubMed DOI

iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition.

IEEE/ACM transactions on computational biology and bioinformatics Apr 6, 2021
Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association,...
Sequence Analysis, Protein Proteins Neural Networks, Computer Histidine Phosphorylation Computational Biology Amino Acid Sequence Models, Statistical
View on PubMed DOI
Popular Topics
Recent Journals