AIMC Topic: Protein Conformation, beta-Strand

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BetaDL: A protein beta-sheet predictor utilizing a deep learning model and independent set solution.

Computers in biology and medicine Dec 2, 2018
The sequence-based prediction of beta-residue contacts and beta-sheet structures contain key information for protein structure prediction. However, the determination of beta-sheet structures poses numerous challenges due to long-range beta-residue in...
Computational Biology Proteins Databases, Protein Models, Molecular Protein Conformation, beta-Strand Software Deep Learning
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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 Antagonists Protein Conformation, beta-Strand Point Mutation Serotonin 5-HT2 Receptor Agonists Animals Binding Sites Protein Binding Protein Engineering Thermodynamics Humans Amino Acid Sequence Protein Interaction Domains and Motifs Machine Learning Protein Stability Protein Conformation, alpha-Helical Sequence Alignment Receptor, Serotonin, 5-HT2C Sequence Homology, Amino Acid Crystallography, X-Ray Models, Molecular Gene Expression Kinetics
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Editorial-Sequences and topology.

Current opinion in structural biology Jun 4, 2017
Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Machine Learning Animals Computational Biology Thermodynamics Protein Interaction Mapping Molecular Docking Simulation Humans Proteins Protein Binding Protein Multimerization Binding Sites
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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 Interaction Domains and Motifs Supervised Machine Learning Protein Conformation, beta-Strand Epitopes, B-Lymphocyte Antigens Models, Statistical Epitope Mapping Protein Conformation, alpha-Helical Binding Sites B-Lymphocytes Humans Protein Binding
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OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method.

Journal of computational biology : a journal of computational molecular cell biology Aug 11, 2016
In the two transmembrane protein types, outer membrane proteins (OMPs) perform diverse important biochemical functions, including substrate transport and passive nutrient uptake and intake. Hence their 3D structures are expected to reveal these funct...
Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Bacterial Outer Membrane Proteins Support Vector Machine Membrane Lipids Databases, Protein Protein Structure, Tertiary Biological Transport
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Unambiguous assignment of kinked-β sheets leads to insights into molecular grammar of reversibility in biomolecular condensates.

Protein science : a publication of the Protein Society Sep 1, 2025
Kinked- sheets are short peptide motifs that appear as distortions in strands and often mediate formation of reversible amyloid fibrils in prion-like proteins. Standard methods for assigning secondary structures cannot distinguish these esoteric mo...
Models, Molecular Amyloid Protein Conformation, beta-Strand Biomolecular Condensates Machine Learning
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Discovery of unconventional and nonintuitive self-assembling peptide materials using experiment-driven machine learning.

Science advances Jun 13, 2025
Prediction of peptide secondary structure is challenging because of complex molecular interactions, sequence-specific behavior, and environmental factors. Traditional design strategies, based on hydrophobicity and structural propensity, can be biased...
Machine Learning Peptides Amino Acid Sequence Hydrophobic and Hydrophilic Interactions Protein Conformation, beta-Strand
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Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes.

Briefings in bioinformatics Sep 2, 2021
Protein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein inte...
Protein Conformation, beta-Strand Software Molecular Docking Simulation Protein Multimerization Deep Learning Protein Interaction Domains and Motifs Datasets as Topic Protein Conformation, alpha-Helical Binding Sites Protein Binding Proteins Humans
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Computational Ion Channel Research: from the Application of Artificial Intelligence to Molecular Dynamics Simulations.

Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology Mar 3, 2021
Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods ha...
Artificial Intelligence Software Animals Protein Binding Humans Quantitative Structure-Activity Relationship Binding Sites Ion Channels Protein Interaction Domains and Motifs Models, Molecular Molecular Dynamics Simulation Ligands Protein Conformation, beta-Strand Ion Channel Gating Membrane Transport Modulators Structural Homology, Protein Protein Conformation, alpha-Helical
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Structures of the β-barrel assembly machine recognizing outer membrane protein substrates.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology Jan 1, 2021
β-barrel outer membrane proteins (β-OMPs) play critical roles in nutrition acquisition, protein import/export, and other fundamental biological processes. The assembly of β-OMPs in Gram-negative bacteria is mediated by the β-barrel assembly machinery...
Bacterial Outer Membrane Proteins Protein Conformation, beta-Strand Machine Learning Protein Domains
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