AIMC Topic: 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...
Attention Crystallization Crystallography, X-Ray Deep Learning Proteins
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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...
Synchrotrons Crystallography Macromolecular Substances Crystallography, X-Ray Humans Artificial Intelligence SARS-CoV-2 COVID-19 Data Mining
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'It will change everything': DeepMind's AI makes gigantic leap in solving protein structures.

Nature Dec 1, 2020
Deep Learning Time Factors Proteins Crystallography, X-Ray Protein Conformation Models, Molecular Caspases
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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 Interaction Mapping Protein Interaction Domains and Motifs Thermodynamics Mutation, Missense Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Internet Benchmarking Crystallography, X-Ray Binding Sites Datasets as Topic Protein Binding Proteins Machine Learning Software Humans
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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...
Crystallography, X-Ray Humans Protein Conformation Databases, Protein Machine Learning Receptors, Fc Algorithms Elasticity Animals Computer Graphics
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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...
Luminescent Proteins Humans Photobleaching Bacterial Proteins Escherichia coli Plasmids Mutation Robotics Photochemistry Crystallography, X-Ray Light Models, Biological HeLa Cells
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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...
Crystallography, X-Ray Anti-HIV Agents Drug Resistance, Viral Computational Biology HIV Protease Drug Discovery Structure-Activity Relationship HIV Infections Humans HIV-1 Machine Learning
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