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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 Mar 1, 2020
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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The PSIPRED Protein Analysis Workbench: 20 years on.

Nucleic acids research Jul 2, 2019
The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 year...
Sequence Alignment Sequence Homology, Amino Acid Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Molecular Sequence Annotation Gene Ontology Binding Sites Protein Conformation, beta-Strand Software Protein Binding Proteins Models, Molecular Internet Amino Acid Sequence History, 21st Century
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mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research Jul 2, 2019
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...
Protein Binding Proteins Internet Benchmarking Humans Machine Learning Software Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Thermodynamics Datasets as Topic Mutation, Missense Crystallography, X-Ray Protein Interaction Mapping Binding Sites Protein Interaction Domains and Motifs
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PrankWeb: a web server for ligand binding site prediction and visualization.

Nucleic acids research Jul 2, 2019
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...
Datasets as Topic Binding Sites Thermodynamics Protein Interaction Domains and Motifs Benchmarking Amino Acid Sequence Ligands Humans Protein Conformation, alpha-Helical Machine Learning Protein Conformation, beta-Strand Software Protein Binding Proteins Internet
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BetaDL: A protein beta-sheet predictor utilizing a deep learning model and independent set solution.

Computers in biology and medicine Jan 1, 2019
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...
Proteins Databases, Protein Models, Molecular Protein Conformation, beta-Strand Software Deep Learning Computational Biology
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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 Crystallography, X-Ray Protein Conformation, alpha-Helical Binding Sites Protein Engineering Protein Conformation, beta-Strand Amino Acid Sequence Thermodynamics Point Mutation Protein Stability Receptor, Serotonin, 5-HT2C Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists
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Editorial-Sequences and topology.

Current opinion in structural biology Jun 1, 2017
Protein Multimerization Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Molecular Docking Simulation Binding Sites Protein Conformation, beta-Strand Protein Binding Humans Thermodynamics Computational Biology Machine Learning Protein Interaction Mapping Animals Proteins
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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...
Protein Interaction Domains and Motifs Epitopes, B-Lymphocyte Humans Protein Conformation, alpha-Helical Protein Binding Models, Statistical Epitope Mapping Protein Conformation, beta-Strand Antigens B-Lymphocytes Supervised Machine Learning Binding Sites Antigen-Antibody Complex
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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 Mar 1, 2017
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 Conformation, alpha-Helical Bacterial Outer Membrane Proteins Protein Conformation, beta-Strand Support Vector Machine Membrane Lipids Databases, Protein Protein Structure, Tertiary Biological Transport Protein Interaction Domains and Motifs
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