AIMC Topic: Protein Conformation, beta-Strand

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Editorial-Sequences and topology.

Current opinion in structural biology Jun 4, 2017
Protein Interaction Domains and Motifs Protein Binding Protein Conformation, alpha-Helical Computational Biology Protein Conformation, beta-Strand Proteins Thermodynamics Binding Sites Humans Protein Interaction Mapping Machine Learning Protein Multimerization Animals Molecular Docking Simulation
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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 Protein Conformation, alpha-Helical Humans Protein Conformation, beta-Strand Binding Sites Protein Binding Models, Statistical Epitope Mapping Antigen-Antibody Complex B-Lymphocytes Protein Interaction Domains and Motifs Supervised Machine Learning Antigens
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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 Conformation, alpha-Helical Bacterial Outer Membrane Proteins Protein Conformation, beta-Strand Support Vector Machine Membrane Lipids Protein Structure, Tertiary Databases, Protein Protein Interaction Domains and Motifs Biological Transport
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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...
Peptides Amino Acid Sequence Hydrophobic and Hydrophilic Interactions Protein Conformation, beta-Strand Machine Learning
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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...
Proteins Datasets as Topic Binding Sites Protein Multimerization Molecular Docking Simulation Deep Learning Protein Binding Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Humans Protein Conformation, beta-Strand Software
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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...
Humans Artificial Intelligence Software Animals Protein Interaction Domains and Motifs Ion Channel Gating Structural Homology, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Membrane Transport Modulators Ligands Quantitative Structure-Activity Relationship Binding Sites Ion Channels Protein Binding Models, Molecular Molecular Dynamics Simulation
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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...
Machine Learning Protein Domains Bacterial Outer Membrane Proteins Protein Conformation, beta-Strand
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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...
Protein Binding Proteins Models, Molecular Internet Amino Acid Sequence History, 21st Century Molecular Sequence Annotation Gene Ontology Software Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Binding Sites Protein Conformation, beta-Strand Sequence Alignment Sequence Homology, Amino Acid
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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 Interaction Mapping Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Binding Sites Thermodynamics Mutation, Missense Machine Learning Humans Software Protein Binding Proteins Internet Benchmarking Datasets as Topic Crystallography, X-Ray
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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...
Thermodynamics Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Ligands Datasets as Topic Binding Sites Humans Machine Learning Software Protein Binding Proteins Internet Benchmarking Amino Acid Sequence
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