AIMC Topic: 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 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 Support Vector Machine Protein Conformation, beta-Strand Membrane Lipids Databases, Protein Protein Structure, Tertiary Biological Transport Protein Interaction Domains and Motifs
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HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures.

Bioinformatics (Oxford, England) Jan 1, 2023
MOTIVATION: Protein and peptide engineering has become an essential field in biomedicine with therapeutics, diagnostics and synthetic biology applications. Helices are both abundant structural feature in proteins and comprise a major portion of bioac...
Deep Learning Proteins Protein Structure, Secondary Protein Conformation, alpha-Helical Peptides
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Computational Approaches for Investigating Disease-causing Mutations in Membrane Proteins: Database Development, Analysis and Prediction.

Current topics in medicinal chemistry Jan 1, 2022
Membrane proteins (MPs) play an essential role in a broad range of cellular functions, serving as transporters, enzymes, receptors, and communicators, and about ~60% of membrane proteins are primarily used as drug targets. These proteins adopt either...
Machine Learning Databases, Factual Databases, Protein Humans Computational Biology Mutation Membrane Proteins Protein Conformation, alpha-Helical
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DeepDTAF: a deep learning method to predict protein-ligand binding affinity.

Briefings in bioinformatics Sep 2, 2021
Biomolecular recognition between ligand and protein plays an essential role in drug discovery and development. However, it is extremely time and resource consuming to determine the protein-ligand binding affinity by experiments. At present, many comp...
Protein Binding Proteins Models, Molecular Amino Acid Sequence Software Reproducibility of Results Drug Discovery Deep Learning Binding Sites Protein Conformation, alpha-Helical Ligands Data Accuracy Hydrogen Bonding
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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, alpha-Helical Protein Conformation, beta-Strand Molecular Docking Simulation Deep Learning Datasets as Topic Humans Protein Binding Software Proteins Binding Sites Protein Multimerization Protein Interaction Domains and Motifs
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Computational studies of anaplastic lymphoma kinase mutations reveal common mechanisms of oncogenic activation.

Proceedings of the National Academy of Sciences of the United States of America Mar 9, 2021
Kinases play important roles in diverse cellular processes, including signaling, differentiation, proliferation, and metabolism. They are frequently mutated in cancer and are the targets of a large number of specific inhibitors. Surveys of cancer gen...
Anaplastic Lymphoma Kinase Molecular Dynamics Simulation Enzyme Activation Protein Conformation, alpha-Helical Humans Machine Learning Mutation
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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...
Structural Homology, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Membrane Transport Modulators Ion Channels Protein Interaction Domains and Motifs Ion Channel Gating Animals Protein Binding Models, Molecular Molecular Dynamics Simulation Ligands Quantitative Structure-Activity Relationship Binding Sites Humans Artificial Intelligence Software
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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...
Gene Ontology Amino Acid Sequence Software Binding Sites History, 21st Century Protein Binding Protein Interaction Domains and Motifs Sequence Alignment Molecular Sequence Annotation Proteins Sequence Homology, Amino Acid Protein Conformation, alpha-Helical Models, Molecular Protein Conformation, beta-Strand Internet
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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 Machine Learning Protein Interaction Domains and Motifs Software Protein Conformation, alpha-Helical Humans Crystallography, X-Ray Protein Binding Protein Conformation, beta-Strand Internet Binding Sites Proteins Thermodynamics Benchmarking Mutation, Missense Datasets as Topic
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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...
Humans Binding Sites Machine Learning Benchmarking Thermodynamics Protein Conformation, beta-Strand Protein Binding Software Protein Interaction Domains and Motifs Amino Acid Sequence Protein Conformation, alpha-Helical Proteins Ligands Internet Datasets as Topic
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