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Crystallography, X-Ray

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Sequence assignment for low-resolution modelling of protein crystal structures.

Acta crystallographica. Section D, Structural biology 31373574
The performance of automated model building in crystal structure determination usually decreases with the resolution of the experimental data, and may result in fragmented models and incorrect side-chain assignment. Presented here are new methods for...
Algorithms Amino Acid Sequence Crystallography, X-Ray Databases, Protein Datasets as Topic Machine Learning Molecular Docking Simulation Protein Conformation Proteins Software
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Machine Learning Models for Accurate Prediction of Kinase Inhibitors with Different Binding Modes.

Journal of medicinal chemistry 31469557
Noncovalent inhibitors of protein kinases have different modes of action. They bind to the active or inactive form of kinases, compete with ATP, stabilize inactive kinase conformations, or act through allosteric sites. Accordingly, kinase inhibitors ...
Crystallography, X-Ray Databases, Chemical Datasets as Topic Machine Learning Protein Binding Protein Kinase Inhibitors Protein Kinases
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Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction.

Scientific reports 31451723
Protein Secondary Structure prediction has been a central topic of research in Bioinformatics for decades. In spite of this, even the most sophisticated ab initio SS predictors are not able to reach the theoretical limit of three-state prediction acc...
Algorithms Computational Biology Crystallography, X-Ray Magnetic Resonance Spectroscopy Neural Networks, Computer Protein Structure, Secondary
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Analysis of distance-based protein structure prediction by deep learning in CASP13.

Proteins 31471916
This paper reports the CASP13 results of distance-based contact prediction, threading, and folding methods implemented in three RaptorX servers, which are built upon the powerful deep convolutional residual neural network (ResNet) method initiated by...
Algorithms Computational Biology Crystallography, X-Ray Deep Learning Machine Learning Models, Molecular Protein Conformation Protein Folding Proteins Sequence Alignment Sequence Analysis, Protein Software
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Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S.

Journal of computer-aided molecular design 31729618
Cathepsin S (CatS), a member of cysteine cathepsin proteases, has been well studied due to its significant role in many pathological processes, including arthritis, cancer and cardiovascular diseases. CatS inhibitors have been included in D3R-GC3 for...
Binding Sites Cathepsins Computer-Aided Design Crystallography, X-Ray Databases, Protein Humans Ligands Machine Learning Molecular Docking Simulation Protein Binding Protein Conformation Thermodynamics
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers.

Progress in molecular biology and translational science 31952685
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfam...
Algorithms Allosteric Site Animals Computational Biology Crystallography, X-Ray Fluorescence Resonance Energy Transfer Humans Ligands Machine Learning Molecular Dynamics Simulation Mutation Neural Networks, Computer Protein Binding Protein Interaction Mapping Protein Multimerization Protein Structure, Secondary Receptors, G-Protein-Coupled Software Support Vector Machine
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Need for Cross-Validation of Single Particle Cryo-EM.

Journal of chemical information and modeling 32101412
Cross-validation is used to determine the validity of a model on unseen data by assessing if the model is overfitted to noise. It is widely used in many fields, from artificial intelligence to structural biology in X-ray crystallography and nuclear m...
Artificial Intelligence Cryoelectron Microscopy Crystallography, X-Ray Signal-To-Noise Ratio
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Predicting protein model correctness in Coot using machine learning.

Acta crystallographica. Section D, Structural biology 32744253
Manually identifying and correcting errors in protein models can be a slow process, but improvements in validation tools and automated model-building software can contribute to reducing this burden. This article presents a new correctness score that ...
Crystallography, X-Ray Machine Learning Models, Molecular Protein Conformation Proteins Software
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'It will change everything': DeepMind's AI makes gigantic leap in solving protein structures.

Nature 33257889
Caspases Crystallography, X-Ray Deep Learning Models, Molecular Protein Conformation Proteins Time Factors
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TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction.

Journal of chemical information and modeling 33464891
Proteins carry out the most fundamental processes of life such as cellular metabolism, regulation, and communication. Understanding these processes at a molecular level requires knowledge of their three-dimensional structures. Experimental techniques...
Crystallography, X-Ray Deep Learning Neural Networks, Computer Protein Conformation Proteins Software
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