AIMC Topic: Protein Folding

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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...
Computational Biology Proteins Artificial Intelligence Deep Learning Mutation, Missense Protein Folding Models, Molecular Protein Conformation Humans
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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...
Protein Folding Protein Structure, Tertiary Ureaplasma urealyticum Models, Molecular Artificial Intelligence Bacterial Proteins Peptides
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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 Mutation Protein Conformation Protein Folding Machine Learning Proteins Sequence Alignment Cluster Analysis Bacterial Proteins
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Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations.

Journal of chemical information and modeling Nov 13, 2023
Despite advances in artificial intelligence methods, protein folding remains in many ways an enigma to be solved. Accurate computation of protein folding energetics could help drive fields such as protein and drug design and genetic interpretation. H...
Thermodynamics Protein Folding Proteins Molecular Dynamics Simulation Artificial Intelligence
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Role of environmental specificity in CASP results.

BMC bioinformatics Nov 11, 2023
BACKGROUND: Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical Assessment of Structure Predict...
Protein Conformation Protein Folding Models, Molecular Hydrophobic and Hydrophilic Interactions Artificial Intelligence Proteins
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ResCNNT-fold: Combining residual convolutional neural network and Transformer for protein fold recognition from language model embeddings.

Computers in biology and medicine Oct 17, 2023
A comprehensive understanding of protein functions holds significant promise for disease research and drug development, and proteins with analogous tertiary structures tend to exhibit similar functions. Protein fold recognition stands as a classical ...
Proteins Databases, Protein Protein Folding Sequence Analysis, Protein Neural Networks, Computer Computational Biology Humans
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SeqPredNN: a neural network that generates protein sequences that fold into specified tertiary structures.

BMC bioinformatics Oct 3, 2023
BACKGROUND: The relationship between the sequence of a protein, its structure, and the resulting connection between its structure and function, is a foundational principle in biological science. Only recently has the computational prediction of prote...
Amino Acids Amino Acid Sequence Protein Folding Neural Networks, Computer Proteins
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Folding and functions of knotted proteins.

Current opinion in structural biology Sep 29, 2023
Topologically knotted proteins have entangled structural elements within their native structures that cannot be disentangled simply by pulling from the N- and C-termini. Systematic surveys have identified different types of knotted protein structures...
Protein Conformation Artificial Intelligence Protein Folding Proteins
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Uncovering new families and folds in the natural protein universe.

Nature Sep 13, 2023
We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database. These models cover nearly all proteins that are known, including thos...
Protein Folding Structural Homology, Protein Amino Acid Sequence Molecular Sequence Annotation Databases, Protein Deep Learning Internet Proteins
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