AIMC Topic: Protein Folding

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AlphaFold2 structures guide prospective ligand discovery.

Science (New York, N.Y.) Jun 21, 2024
AlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ and serotonin 2A (5-HT2A) receptors, testing hundreds of new molecules a...
Ligands Receptor, Serotonin, 5-HT2A Protein Conformation Drug Discovery Deep Learning Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists Receptors, sigma Cryoelectron Microscopy Small Molecule Libraries Humans Protein Folding Molecular Docking Simulation Drug Design
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Computational design of soluble and functional membrane protein analogues.

Nature Jun 19, 2024
De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topolog...
Deep Learning Proteome Membrane Proteins Humans Computer-Aided Design Protein Stability Proof of Concept Study Protein Folding Receptors, G-Protein-Coupled Models, Molecular Solubility Amino Acid Motifs
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Folding the human proteome using BioNeMo: A fused dataset of structural models for machine learning purposes.

Scientific data Jun 6, 2024
Human proteins are crucial players in both health and disease. Understanding their molecular landscape is a central topic in biological research. Here, we present an extensive dataset of predicted protein structures for 42,042 distinct human proteins...
Models, Molecular Protein Conformation Protein Folding Machine Learning Humans Proteome Databases, Protein
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Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences.

Proteins May 29, 2024
We apply methods of Artificial Intelligence and Machine Learning to protein dynamic bioinformatics. We rewrite the sequences of a large protein data set, containing both folded and intrinsically disordered molecules, using a representation developed ...
Databases, Protein Amino Acid Sequence Intrinsically Disordered Proteins Fourier Analysis Protein Folding Sequence Analysis, Protein Algorithms Computational Biology Proteins Artificial Intelligence Machine Learning
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One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates.

The journal of physical chemistry. B Apr 3, 2024
Identifying optimal reaction coordinates for complex conformational changes and protein folding remains an outstanding challenge. This study combines collective variable (CV) discovery based on chemical intuition and machine learning with enhanced sa...
Machine Learning Peptides Discriminant Analysis Molecular Dynamics Simulation Thermodynamics Protein Folding
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Recent Progress of Protein Tertiary Structure Prediction.

Molecules (Basel, Switzerland) Feb 13, 2024
The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades. Recently, the widespread integration of artificial intelligence (AI)...
Artificial Intelligence Software Algorithms Models, Molecular Computational Biology Protein Conformation Proteins Protein Folding Databases, Protein
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Prediction of protein structure and AI.

Journal of human genetics Jan 4, 2024
AlphaFold, an artificial intelligence (AI)-based tool for predicting the 3D structure of proteins, is now widely recognized for its high accuracy and versatility in the folding of human proteins. AlphaFold is useful for understanding structure-functi...
Humans Artificial Intelligence Proteins Mutation, Missense Deep Learning Models, Molecular Computational Biology Protein Folding Protein Conformation
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Recent Advances and Challenges in Protein Structure Prediction.

Journal of chemical information and modeling Dec 18, 2023
Artificial intelligence has made significant advances in the field of protein structure prediction in recent years. In particular, DeepMind's end-to-end model, AlphaFold2, has demonstrated the capability to predict three-dimensional structures of num...
Drug Discovery Protein Folding Artificial Intelligence Research Design
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Structure, dynamics, and stability of the smallest and most complex 7 protein knot.

The Journal of biological chemistry Dec 10, 2023
Proteins can spontaneously tie a variety of intricate topological knots through twisting and threading of the polypeptide chains. Recently developed artificial intelligence algorithms have predicted several new classes of topological knotted proteins...
Artificial Intelligence Peptides Models, Molecular Ureaplasma urealyticum Bacterial Proteins Protein Folding Protein Structure, Tertiary
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Predicting multiple conformations via sequence clustering and AlphaFold2.

Nature Nov 13, 2023
AlphaFold2 (ref. ) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends on multiple conformational substates, and disease-causing point mutations often ca...
Rhodobacter sphaeroides Protein Conformation Machine Learning Proteins Protein Folding Bacterial Proteins Cluster Analysis Sequence Alignment Mutation
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