AIMC Topic: Protein Conformation

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Accurate prediction of protein structures and interactions using a three-track neural network.

Science (New York, N.Y.) Jul 15, 2021
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track ...
Deep Learning Membrane Proteins Proteins Neural Networks, Computer Computer Simulation Amino Acid Sequence ADAM Proteins Crystallography, X-Ray Databases, Protein Receptors, G-Protein-Coupled Models, Molecular Multiprotein Complexes Protein Subunits Sphingosine N-Acyltransferase Protein Conformation Cryoelectron Microscopy Protein Folding
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Highly accurate protein structure prediction with AlphaFold.

Nature Jul 15, 2021
Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort, the structures of around 100,000 unique proteins have been determined, but this r...
Protein Folding Sequence Alignment Models, Molecular Amino Acid Sequence Protein Conformation Computational Biology Proteins Databases, Protein Neural Networks, Computer Reproducibility of Results Deep Learning
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SidechainNet: An all-atom protein structure dataset for machine learning.

Proteins Jul 12, 2021
Despite recent advancements in deep learning methods for protein structure prediction and representation, little focus has been directed at the simultaneous inclusion and prediction of protein backbone and sidechain structure information. We present ...
Neural Networks, Computer Amino Acids Amino Acid Sequence Machine Learning Datasets as Topic Software Protein Conformation Proteins
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Physics-based protein structure refinement in the era of artificial intelligence.

Proteins Jun 29, 2021
Protein structure refinement is the last step in protein structure prediction pipelines. Physics-based refinement via molecular dynamics (MD) simulations has made significant progress during recent years. During CASP14, we tested a new refinement pro...
Markov Chains Protein Conformation Physical Phenomena Artificial Intelligence Software Computational Biology Proteins Molecular Dynamics Simulation
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TopDomain: Exhaustive Protein Domain Boundary Metaprediction Combining Multisource Information and Deep Learning.

Journal of chemical theory and computation Jun 23, 2021
Protein domains are independent, functional, and stable structural units of proteins. Accurate protein domain boundary prediction plays an important role in understanding protein structure and evolution, as well as for protein structure prediction. C...
Protein Conformation Computational Biology Proteins Protein Domains Algorithms Deep Learning
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Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations.

Cell reports methods Jun 21, 2021
Structure prediction for proteins lacking homologous templates in the Protein Data Bank (PDB) remains a significant unsolved problem. We developed a protocol, C-I-TASSER, to integrate interresidue contact maps from deep neural-network learning with t...
Humans Deep Learning Computational Biology Proteins Models, Molecular COVID-19 Protein Conformation Algorithms SARS-CoV-2
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AlphaFold - A Personal Perspective on the Impact of Machine Learning.

Journal of molecular biology Jun 2, 2021
I outline how over my career as a protein scientist Machine Learning has impacted my area of science and one of my pastimes, chess, where there are some interesting parallels. In 1968, modelling of three-dimensional structures was initiated based on ...
Protein Folding Animals Proteins Models, Molecular Protein Conformation Trypsin Chymotrypsin Humans Machine Learning Software
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Recent Applications of Deep Learning Methods on Evolution- and Contact-Based Protein Structure Prediction.

International journal of molecular sciences Jun 2, 2021
The new advances in deep learning methods have influenced many aspects of scientific research, including the study of the protein system. The prediction of proteins' 3D structural components is now heavily dependent on machine learning techniques tha...
Deep Learning Computational Biology Evolution, Molecular Databases, Protein Amino Acid Sequence Protein Conformation Neural Networks, Computer Machine Learning Humans Sequence Alignment Software
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Protein Structure Prediction: Conventional and Deep Learning Perspectives.

The protein journal May 28, 2021
Protein structure prediction is a way to bridge the sequence-structure gap, one of the main challenges in computational biology and chemistry. Predicting any protein's accurate structure is of paramount importance for the scientific community, as the...
Databases, Protein Protein Conformation Deep Learning Computational Biology Proteins Software
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VirtualFlow Ants-Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization.

International journal of molecular sciences May 28, 2021
The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and th...
Ligands Molecular Docking Simulation Artificial Intelligence Thermodynamics Protein Conformation Algorithms Protein Binding NF-E2-Related Factor 2 Kelch-Like ECH-Associated Protein 1 Reproducibility of Results Computational Biology
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