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Protein Conformation, alpha-Helical

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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 27513917
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...
Bacterial Outer Membrane Proteins Biological Transport Databases, Protein Membrane Lipids Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Protein Structure, Tertiary Support Vector Machine
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TMSEG: Novel prediction of transmembrane helices.

Proteins 27566436
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...
Databases, Protein Datasets as Topic Humans Hydrophobic and Hydrophilic Interactions Machine Learning Membrane Proteins Protein Conformation, alpha-Helical Sensitivity and Specificity
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Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences.

BMC genomics 28361709
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 Antigens B-Lymphocytes Binding Sites Epitope Mapping Epitopes, B-Lymphocyte Humans Models, Statistical Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Supervised Machine Learning
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Editorial-Sequences and topology.

Current opinion in structural biology 28587734
Animals Binding Sites Computational Biology Humans Machine Learning Molecular Docking Simulation Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Multimerization Proteins Thermodynamics
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Predicting the helix-helix interactions from correlated residue mutations.

Proteins 28833538
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 Computational Biology Machine Learning Membrane Proteins Protein Binding Protein Conformation, alpha-Helical Protein Interaction Domains and Motifs
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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife 29927385
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...
Amino Acid Sequence Animals Binding Sites Crystallography, X-Ray Gene Expression Humans Kinetics Machine Learning Models, Molecular Point Mutation Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Engineering Protein Interaction Domains and Motifs Protein Stability Receptor, Serotonin, 5-HT2C Sequence Alignment Sequence Homology, Amino Acid Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists Thermodynamics
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PiPred - a deep-learning method for prediction of π-helices in protein sequences.

Scientific reports 31053765
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...
Amino Acid Sequence Computational Biology Deep Learning Models, Molecular Protein Conformation, alpha-Helical Proteins
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mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research 31114883
Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predic...
Benchmarking Binding Sites Crystallography, X-Ray Datasets as Topic Humans Internet Machine Learning Mutation, Missense Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Protein Interaction Mapping Proteins Software Thermodynamics
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PrankWeb: a web server for ligand binding site prediction and visualization.

Nucleic acids research 31114880
PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability cent...
Amino Acid Sequence Benchmarking Binding Sites Datasets as Topic Humans Internet Ligands Machine Learning Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Proteins Software Thermodynamics
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