AIMC Topic: Protein Conformation, alpha-Helical

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TMSEG: Novel prediction of transmembrane helices.

Proteins Sep 16, 2016
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...
Protein Conformation, alpha-Helical Databases, Protein Hydrophobic and Hydrophilic Interactions Sensitivity and Specificity Datasets as Topic Membrane Proteins Humans Machine Learning
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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...
Bacterial Outer Membrane Proteins Membrane Lipids Protein Structure, Tertiary Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Support Vector Machine Protein Conformation, beta-Strand Databases, Protein Biological Transport
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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 Peptides Protein Structure, Secondary Protein Conformation, alpha-Helical
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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...
Databases, Factual Computational Biology Membrane Proteins Databases, Protein Humans Machine Learning Mutation 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...
Software Reproducibility of Results Drug Discovery Models, Molecular Amino Acid Sequence Ligands Data Accuracy Deep Learning Protein Binding Proteins Hydrogen Bonding Binding Sites Protein Conformation, alpha-Helical
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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 Binding Protein Conformation, beta-Strand Proteins Datasets as Topic Protein Interaction Domains and Motifs Humans Binding Sites Protein Conformation, alpha-Helical Molecular Docking Simulation Software Protein Multimerization Deep Learning
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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...
Humans Machine Learning Mutation Protein Conformation, alpha-Helical Molecular Dynamics Simulation Anaplastic Lymphoma Kinase Enzyme Activation
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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...
Membrane Transport Modulators Structural Homology, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Molecular Dynamics Simulation Ligands Animals Quantitative Structure-Activity Relationship Protein Binding Models, Molecular Protein Interaction Domains and Motifs Humans Binding Sites Ion Channel Gating Artificial Intelligence Ion Channels 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...
Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Software Sequence Alignment Protein Binding Sequence Homology, Amino Acid History, 21st Century Proteins Protein Interaction Domains and Motifs Molecular Sequence Annotation Models, Molecular Gene Ontology Internet Binding Sites Amino Acid Sequence
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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...
Software Protein Binding Proteins Protein Interaction Mapping Datasets as Topic Binding Sites Protein Conformation, alpha-Helical Internet Protein Interaction Domains and Motifs Humans Crystallography, X-Ray Thermodynamics Benchmarking Protein Conformation, beta-Strand Machine Learning Mutation, Missense
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