AIMC Topic: Protein Conformation

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Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.

Briefings in bioinformatics Mar 10, 2022
With the rapid progress of deep learning in cryo-electron microscopy and protein structure prediction, improving the accuracy of the protein structure model by using a density map and predicted contact/distance map through deep learning has become an...
Models, Molecular Protein Conformation Cryoelectron Microscopy Deep Learning Membrane Proteins
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Protein-RNA interaction prediction with deep learning: structure matters.

Briefings in bioinformatics Jan 17, 2022
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Because of the limitation of the previous database, especially the lac...
Computational Biology Algorithms Protein Conformation RNA-Binding Proteins Deep Learning Binding Sites RNA
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OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors.

Briefings in bioinformatics Jan 17, 2022
Accurate protein side-chain modeling is crucial for protein folding and protein design. In the past decades, many successful methods have been proposed to address this issue. However, most of them depend on the discrete samples from the rotamer libra...
Protein Conformation Gene Library Protein Folding Cell Differentiation Models, Molecular Computational Biology Deep Learning Proteins
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Deep learning and protein structure modeling.

Nature methods Jan 1, 2022
Algorithms Deep Learning Computational Biology Protein Conformation Sequence Alignment Multiprotein Complexes Proteins Models, Molecular
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Solving Protein Structure with AI: Viva AlphaFold and Co.!

Current protein & peptide science Dec 27, 2021
Proteins Protein Conformation Artificial Intelligence
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Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics.

Bioinformatics (Oxford, England) Dec 7, 2021
MOTIVATION: The investigation of the structure of biological systems at the molecular level gives insights about their functions and dynamics. Shape and surface of biomolecules are fundamental to molecular recognition events. Characterizing their geo...
Protein Folding Sequence Analysis, Protein Artificial Intelligence Computational Biology Datasets as Topic Protein Conformation Databases, Protein
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Predicting Proteome-Scale Protein Structure with Artificial Intelligence.

The New England journal of medicine Dec 2, 2021
Artificial Intelligence Computer Simulation Proteome Databases, Protein Computational Biology Humans Protein Conformation
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Applying and improving AlphaFold at CASP14.

Proteins Dec 1, 2021
We describe the operation and improvement of AlphaFold, the system that was entered by the team AlphaFold2 to the "human" category in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The AlphaFold system entered in CASP14 is ent...
Protein Folding Software Amino Acid Sequence Deep Learning Sequence Analysis, Protein Protein Conformation Proteins Neural Networks, Computer Models, Molecular Computational Biology
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Improving protein fold recognition using triplet network and ensemble deep learning.

Briefings in bioinformatics Nov 5, 2021
Protein fold recognition is a critical step toward protein structure and function prediction, aiming at providing the most likely fold type of the query protein. In recent years, the development of deep learning (DL) technique has led to massive adva...
Protein Conformation Protein Folding Reproducibility of Results Deep Learning Databases, Protein Proteins Sensitivity and Specificity Neural Networks, Computer Computational Biology Models, Molecular Algorithms
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Machine learning builds full-QM precision protein force fields in seconds.

Briefings in bioinformatics Nov 5, 2021
Full-quantum mechanics (QM) calculations are extraordinarily precise but difficult to apply to large systems, such as biomolecules. Motivated by the massive demand for efficient calculations for large systems at the full-QM level and by the significa...
Protein Conformation Molecular Dynamics Simulation Quantum Theory Neural Networks, Computer Computational Biology Machine Learning Proteins Reproducibility of Results Algorithms Databases, Protein Peptides
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