AIMC Topic: Crystallography, X-Ray

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Ligand identification in CryoEM and X-ray maps using deep learning.

Bioinformatics (Oxford, England) Dec 26, 2024
MOTIVATION: Accurately identifying ligands plays a crucial role in the process of structure-guided drug design. Based on density maps from X-ray diffraction or cryogenic-sample electron microscopy (cryoEM), scientists verify whether small-molecule li...
Ligands Crystallography, X-Ray Cryoelectron Microscopy Drug Design Deep Learning Models, Molecular
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NucleoFind: a deep-learning network for interpreting nucleic acid electron density.

Nucleic acids research Sep 23, 2024
Nucleic acid electron density interpretation after phasing by molecular replacement or other methods remains a difficult problem for computer programs to deal with. Programs tend to rely on time-consuming and computationally exhaustive searches to re...
Nucleic Acids Crystallography, X-Ray Nucleic Acid Conformation Deep Learning Models, Molecular Electrons Software
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Assessment of Protein-Protein Docking Models Using Deep Learning.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2024
Protein-protein interactions are involved in almost all processes in a living cell and determine the biological functions of proteins. To obtain mechanistic understandings of protein-protein interactions, the tertiary structures of protein complexes ...
Molecular Docking Simulation Deep Learning Computational Biology Protein Conformation Protein Binding Software Protein Interaction Mapping Proteins Crystallography, X-Ray
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SADeepcry: a deep learning framework for protein crystallization propensity prediction using self-attention and auto-encoder networks.

Briefings in bioinformatics Sep 20, 2022
The X-ray diffraction (XRD) technique based on crystallography is the main experimental method to analyze the three-dimensional structure of proteins. The production process of protein crystals on which the XRD technique relies has undergone multiple...
Deep Learning Proteins Attention Crystallization Crystallography, X-Ray
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Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Like an article narrative is deemed by an editor and referees to be worthy of being a version of record on acceptance as a publication, so must the underpinning data also be scrutinized before passing it as a version of record. Indeed without the und...
SARS-CoV-2 Data Mining Macromolecular Substances Humans Artificial Intelligence COVID-19 Crystallography, X-Ray Synchrotrons Crystallography
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'It will change everything': DeepMind's AI makes gigantic leap in solving protein structures.

Nature Dec 1, 2020
Time Factors Proteins Models, Molecular Caspases Crystallography, X-Ray Protein Conformation Deep Learning
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mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research Jul 2, 2019
Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predic...
Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Mapping Protein Interaction Domains and Motifs Benchmarking Datasets as Topic Crystallography, X-Ray Binding Sites Thermodynamics Mutation, Missense Humans Protein Binding Machine Learning Proteins Software Internet
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Blind prediction of protein B-factor and flexibility.

The Journal of chemical physics Oct 7, 2018
The Debye-Waller factor, a measure of X-ray attenuation, can be experimentally observed in protein X-ray crystallography. Previous theoretical models have made strong inroads in the analysis of beta (B)-factors by linearly fitting protein B-factors f...
Databases, Protein Elasticity Crystallography, X-Ray Protein Conformation Computer Graphics Receptors, Fc Machine Learning Algorithms Animals Humans
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Enhancing fluorescent protein photostability through robot-assisted photobleaching.

Integrative biology : quantitative biosciences from nano to macro Jul 16, 2018
Improving fluorescent proteins through the use of directed evolution requires robust techniques for screening large libraries of genetic variants. Here we describe an effective and relatively low-cost system for screening libraries of fluorescent pro...
Photochemistry Bacterial Proteins Humans Crystallography, X-Ray Light Mutation Luminescent Proteins Escherichia coli Models, Biological HeLa Cells Photobleaching Robotics Plasmids
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Tackling the problem of HIV drug resistance.

Postepy biochemii Jan 1, 2016
The virally-encoded HIV-1 protease is an effective target for antiviral drugs, however, treatment for HIV infections is limited by the prevalence of drug resistant viral mutants. In this review, we describe our three-pronged approach to analyze and c...
Computational Biology Structure-Activity Relationship Drug Discovery Drug Resistance, Viral HIV-1 Humans HIV Protease HIV Infections Machine Learning Crystallography, X-Ray Anti-HIV Agents
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