AIMC Topic: Protein Conformation

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Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies.

Nature communications Apr 25, 2023
Antibodies have the capacity to bind a diverse set of antigens, and they have become critical therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six hypervariable loops that are diversified through genetic rec...
Deep Learning Antigens Complementarity Determining Regions Antibodies Protein Conformation
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Exploiting conformational dynamics to modulate the function of designed proteins.

Proceedings of the National Academy of Sciences of the United States of America Apr 24, 2023
With the recent success in calculating protein structures from amino acid sequences using artificial intelligence-based algorithms, an important next step is to decipher how dynamics is encoded by the primary protein sequence so as to better predict ...
Artificial Intelligence Proteins Ligands Amino Acid Sequence Peptides Protein Conformation
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Enhancing Conformational Sampling for Intrinsically Disordered and Ordered Proteins by Variational Autoencoder.

International journal of molecular sciences Apr 7, 2023
Intrinsically disordered proteins (IDPs) account for more than 50% of the human proteome and are closely associated with tumors, cardiovascular diseases, and neurodegeneration, which have no fixed three-dimensional structure under physiological condi...
Protein Conformation Humans Magnetic Resonance Spectroscopy Artificial Intelligence Molecular Dynamics Simulation Intrinsically Disordered Proteins
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CryoRes: Local Resolution Estimation of Cryo-EM Density Maps by Deep Learning.

Journal of molecular biology Mar 24, 2023
Recent progress in cryo-EM research has ignited a revolution in biological macromolecule structure determination. Resolution is an essential parameter for quality assessment of a cryo-EM density map, and it is known that resolution varies in differen...
Algorithms Deep Learning Models, Molecular Macromolecular Substances Protein Conformation Cryoelectron Microscopy
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iQDeep: an integrated web server for protein scoring using multiscale deep learning models.

Journal of molecular biology Mar 23, 2023
The remarkable recent advances in protein structure prediction have enabled computational modeling of protein structures with considerably higher accuracy than ever before. While state-of-the-art structure prediction methods provide self-assessment c...
Protein Conformation Sequence Analysis, Protein Computational Biology Software Proteins Deep Learning
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Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning.

Nature biotechnology Mar 20, 2023
While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of...
Protein Conformation Algorithms Deep Learning Mass Spectrometry Proteins
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Evolutionary-scale prediction of atomic-level protein structure with a language model.

Science (New York, N.Y.) Mar 16, 2023
Recent advances in machine learning have leveraged evolutionary information in multiple sequence alignments to predict protein structure. We demonstrate direct inference of full atomic-level protein structure from primary sequence using a large langu...
Proteins Amino Acid Sequence Protein Conformation Sequence Analysis, Protein Machine Learning Evolution, Molecular
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Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures.

Journal of chemical information and modeling Mar 9, 2023
Machine learning-based protein structure prediction algorithms, such as RosettaFold and AlphaFold2, have greatly impacted the structural biology field, arousing a fair amount of discussion around their potential role in drug discovery. While there ar...
Deep Learning Protein Binding Algorithms Molecular Docking Simulation Protein Conformation Proteins Ligands
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Real-to-bin conversion for protein residue distances.

Computational biology and chemistry Feb 25, 2023
Protein Structure Prediction (PSP) has achieved significant progress lately. Prediction of inter-residue distances by machine learning and their exploitation during the conformational search is largely among the critical factors behind the progress. ...
Proteins Algorithms Machine Learning Models, Molecular Databases, Protein Computational Biology Protein Conformation
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Evaluating native-like structures of RNA-protein complexes through the deep learning method.

Nature communications Feb 24, 2023
RNA-protein complexes underlie numerous cellular processes, including basic translation and gene regulation. The high-resolution structure determination of the RNA-protein complexes is essential for elucidating their functions. Therefore, computation...
Deep Learning Protein Binding Algorithms Molecular Docking Simulation RNA Protein Conformation Proteins Models, Molecular
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