AIMC Topic: Protein Folding

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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 Artificial Intelligence Proteins Molecular Dynamics Simulation
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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...
Artificial Intelligence Proteins Protein Conformation Protein Folding Models, Molecular Hydrophobic and Hydrophilic Interactions
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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 ...
Humans Neural Networks, Computer Sequence Analysis, Protein Databases, Protein Protein Folding Computational Biology Proteins
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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...
Proteins Amino Acids Neural Networks, Computer Amino Acid Sequence Protein Folding
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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 Folding Artificial Intelligence Proteins Protein Conformation
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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...
Structural Homology, Protein Internet Amino Acid Sequence Molecular Sequence Annotation Protein Folding Proteins Databases, Protein Deep Learning
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An end-to-end deep learning method for protein side-chain packing and inverse folding.

Proceedings of the National Academy of Sciences of the United States of America May 30, 2023
Protein side-chain packing (PSCP), the task of determining amino acid side-chain conformations given only backbone atom positions, has important applications to protein structure prediction, refinement, and design. Many methods have been proposed to ...
Deep Learning Protein Folding Molecular Conformation Proteins Protein Conformation Amino Acids
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Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning.

Journal of chemical information and modeling Dec 19, 2022
Intrinsically disordered proteins (IDPs) are proteins without a fixed three-dimensional (3D) structure under physiological conditions and are associated with Parkinson's disease, Alzheimer's disease, cancer, cardiovascular disease, amyloidosis, diabe...
Molecular Dynamics Simulation Intrinsically Disordered Proteins Alzheimer Disease Protein Folding Humans Protein Conformation Deep Learning
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Fast and accurate Ab Initio Protein structure prediction using deep learning potentials.

PLoS computational biology Sep 16, 2022
Despite the immense progress recently witnessed in protein structure prediction, the modeling accuracy for proteins that lack sequence and/or structure homologs remains to be improved. We developed an open-source program, DeepFold, which integrates s...
Computational Biology Protein Conformation Proteins Protein Folding Software Algorithms Databases, Protein Models, Molecular Deep Learning
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AlphaFold, Artificial Intelligence (AI), and Allostery.

The journal of physical chemistry. B Aug 17, 2022
AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of biological sequence data and artificial intelligence (AI). AlphaFold has appended projects and research directions. The database it has been creating promises a...
Protein Conformation Allosteric Regulation Molecular Dynamics Simulation Humans Protein Folding Intrinsically Disordered Proteins Artificial Intelligence
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