AIMC Topic: Protein Conformation, alpha-Helical

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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...
Models, Molecular Amino Acids Protein Structure, Secondary Protein Conformation, alpha-Helical 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...
Protein Interaction Domains and Motifs Structural Homology, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Amino Acid Sequence Protein Binding Computer Graphics Research Design Ligands Proteins Protein Interaction Mapping Binding Sites Peptides Protein Multimerization Benchmarking Thermodynamics Molecular Docking Simulation Deep Learning Humans Software
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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...
Computational Biology Proteins Protein Folding Protein Conformation, alpha-Helical Humans Machine Learning Animals Protein Conformation, beta-Strand
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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...
Support Vector Machine Sequence Analysis, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Humans Animals
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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...
Protein Conformation, alpha-Helical Deep Learning Computational Biology Proteins Models, Molecular Amino Acid Sequence
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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...
Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Point Mutation Thermodynamics Sequence Alignment Sequence Homology, Amino Acid Kinetics Amino Acid Sequence Animals Receptor, Serotonin, 5-HT2C Protein Stability Humans Protein Binding Crystallography, X-Ray Machine Learning Models, Molecular Binding Sites Gene Expression Protein Engineering
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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...
Machine Learning Protein Binding Computational Biology Membrane Proteins Amino Acid Sequence Binding Sites Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical
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Editorial-Sequences and topology.

Current opinion in structural biology Jun 4, 2017
Protein Multimerization Molecular Docking Simulation Binding Sites Protein Interaction Domains and Motifs Protein Binding Thermodynamics Protein Conformation, alpha-Helical Humans Computational Biology Protein Interaction Mapping Protein Conformation, beta-Strand Machine Learning Proteins Animals
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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...
Epitopes, B-Lymphocyte Humans Protein Conformation, alpha-Helical Models, Statistical Protein Binding Binding Sites Protein Conformation, beta-Strand B-Lymphocytes Antigen-Antibody Complex Supervised Machine Learning Epitope Mapping Protein Interaction Domains and Motifs Antigens
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TMSEG: Novel prediction of transmembrane helices.

Proteins Sep 16, 2016
Transmembrane proteins (TMPs) are important drug targets because they are essential for signaling, regulation, and transport. Despite important breakthroughs, experimental structure determination remains challenging for TMPs. Various methods have bri...
Protein Conformation, alpha-Helical Membrane Proteins Humans Databases, Protein Machine Learning Hydrophobic and Hydrophilic Interactions Sensitivity and Specificity Datasets as Topic
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