AIMC Topic: Crystallography, X-Ray

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KINNTREX: a neural network to unveil protein mechanisms from time-resolved X-ray crystallography.

IUCrJ May 1, 2024
Here, a machine-learning method based on a kinetically informed neural network (NN) is introduced. The proposed method is designed to analyze a time series of difference electron-density maps from a time-resolved X-ray crystallographic experiment. Th...
Neural Networks, Computer Machine Learning Crystallography, X-Ray Photoreceptors, Microbial Kinetics Bacterial Proteins
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Deep residual networks for crystallography trained on synthetic data.

Acta crystallographica. Section D, Structural biology Jan 1, 2024
The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and tra...
Synchrotrons Algorithms Artificial Intelligence Computer Simulation Crystallography, X-Ray
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The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions.

Acta crystallographica. Section D, Structural biology Nov 3, 2023
Model building and refinement, and the validation of their correctness, are very effective and reliable at local resolutions better than about 2.5 Å for both crystallography and cryo-EM. However, at local resolutions worse than 2.5 Å both the procedu...
Proteins Models, Molecular Peptides Artificial Intelligence Protein Conformation Cryoelectron Microscopy Crystallography, X-Ray
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Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics.

Molecules (Basel, Switzerland) Oct 19, 2023
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interacti...
Crystallography, X-Ray Cryoelectron Microscopy Microscopy, Electron Humans Membrane Proteins Artificial Intelligence
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Facing the phase problem.

IUCrJ Sep 1, 2023
The marvel of X-ray crystallography is the beauty and precision of the atomic structures deduced from diffraction patterns. Since these patterns record only amplitudes, phases for the diffracted waves must also be evaluated for systematic structure d...
Crystallography, X-Ray Explosive Agents Databases, Protein Genomics Artificial Intelligence
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The current role and evolution of X-ray crystallography in drug discovery and development.

Expert opinion on drug discovery Aug 17, 2023
INTRODUCTION: Macromolecular X-ray crystallography and cryo-EM are currently the primary techniques used to determine the three-dimensional structures of proteins, nucleic acids, and viruses. Structural information has been critical to drug discovery...
Crystallography, X-Ray Proteins Drug Discovery Computational Biology Artificial Intelligence Humans
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AlphaFold and the future of structural biology.

Acta crystallographica. Section D, Structural biology Jul 1, 2023
This editorial acknowledges the transformative impact of new machine-learning methods, such as the use of AlphaFold, but also makes the case for the continuing need for experimental structural biology.
Biology Protein Conformation Crystallography, X-Ray Machine Learning Cryoelectron Microscopy
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AlphaFold and the future of structural biology.

IUCrJ Jul 1, 2023
This editorial acknowledges the transformative impact of new machine-learning methods, such as the use of AlphaFold, but also makes the case for the continuing need for experimental structural biology.
Cryoelectron Microscopy Crystallography, X-Ray Biology Machine Learning
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Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology.

Journal of chemical information and modeling Jun 12, 2023
The recent breakthrough made in the field of three-dimensional (3D) structure prediction by artificial intelligence softwares, such as initially AlphaFold2 (AF2) and RosettaFold (RF) and more recently large Language Models (LLM), has revolutionized t...
Biology Crystallography, X-Ray Software Artificial Intelligence
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High-Throughput Screening to Obtain Crystal Hits for Protein Crystallography.

Journal of visualized experiments : JoVE Mar 10, 2023
X-ray crystallography is the most commonly employed technique to discern macromolecular structures, but the crucial step of crystallizing a protein into an ordered lattice amenable to diffraction remains challenging. The crystallization of biomolecul...
High-Throughput Screening Assays Artificial Intelligence Crystallography, X-Ray Reproducibility of Results Proteins
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