AIMC Topic: Protein Conformation, alpha-Helical

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DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures.

Proteins Sep 16, 2020
Accurate prediction of protein secondary structure (alpha-helix, beta-strand and coil) is a crucial step for protein inter-residue contact prediction and ab initio tertiary structure prediction. In a previous study, we developed a deep belief network...
Neural Networks, Computer Software Deep Learning Sequence Alignment Sequence Homology, Amino Acid Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Proteins Databases, Protein Amino Acid Sequence Markov Chains
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A deep attention network for predicting amino acid signals in the formation of [Formula: see text]-helices.

Journal of bioinformatics and computational biology Aug 6, 2020
The secondary and tertiary structure of a protein has a primary role in determining its function. Even though many folding prediction algorithms have been developed in the past decades - mainly based on the assumption that folding instructions are en...
Protein Conformation, alpha-Helical Models, Molecular Amino Acids Protein Structure, Secondary Machine Learning Software Databases, Protein
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Energy-based graph convolutional networks for scoring protein docking models.

Proteins Mar 16, 2020
Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational alternative for su...
Humans Deep Learning Protein Binding Proteins Benchmarking Software Research Design Peptides Molecular Docking Simulation Protein Interaction Domains and Motifs Structural Homology, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Thermodynamics Computer Graphics Protein Interaction Mapping Protein Multimerization Amino Acid Sequence Ligands Binding Sites
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High-accuracy protein structures by combining machine-learning with physics-based refinement.

Proteins Nov 15, 2019
Protein structure prediction has long been available as an alternative to experimental structure determination, especially via homology modeling based on templates from related sequences. Recently, models based on distance restraints from coevolution...
Protein Folding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Animals Computational Biology Proteins Humans Machine Learning
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A step-by-step classification algorithm of protein secondary structures based on double-layer SVM model.

Genomics Nov 15, 2019
In this paper, a step-by-step classification algorithm based on double-layer SVM model is constructed to predict the secondary structure of proteins. The most important feature of this algorithm is to improve the prediction accuracy of α+β and α/β cl...
Animals Support Vector Machine Sequence Analysis, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Humans
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PiPred - a deep-learning method for prediction of π-helices in protein sequences.

Scientific reports May 3, 2019
Canonical π-helices are short, relatively unstable secondary structure elements found in proteins. They comprise seven or more residues and are present in 15% of all known protein structures, often in functionally important regions such as ligand- an...
Models, Molecular Amino Acid Sequence Protein Conformation, alpha-Helical Deep Learning Computational Biology Proteins
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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife Jun 21, 2018
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
Humans Machine Learning Animals Protein Binding Models, Molecular Gene Expression Kinetics Sequence Alignment Sequence Homology, Amino Acid Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Point Mutation Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists Crystallography, X-Ray Binding Sites Protein Engineering Thermodynamics Amino Acid Sequence Protein Stability Receptor, Serotonin, 5-HT2C
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Predicting the helix-helix interactions from correlated residue mutations.

Proteins Aug 24, 2017
Helix-helix interactions are crucial in the structure assembly, stability and function of helix-rich proteins including many membrane proteins. In spite of remarkable progresses over the past decades, the accuracy of predicting protein structures fro...
Amino Acid Sequence Binding Sites Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Binding Computational Biology Membrane Proteins Machine Learning
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Editorial-Sequences and topology.

Current opinion in structural biology Jun 4, 2017
Protein Binding Computational Biology Protein Interaction Domains and Motifs Humans Proteins Protein Conformation, alpha-Helical Binding Sites Protein Conformation, beta-Strand Machine Learning Animals Thermodynamics Molecular Docking Simulation Protein Interaction Mapping Protein Multimerization
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Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences.

BMC genomics Mar 14, 2017
BACKGROUND: The broad heterogeneity of antigen-antibody interactions brings tremendous challenges to the design of a widely applicable learning algorithm to identify conformational B-cell epitopes. Besides the intrinsic heterogeneity introduced by di...
Antigen-Antibody Complex Protein Conformation, alpha-Helical Humans B-Lymphocytes Protein Interaction Domains and Motifs Protein Conformation, beta-Strand Protein Binding Supervised Machine Learning Epitopes, B-Lymphocyte Epitope Mapping Models, Statistical Antigens Binding Sites
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