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Crystallography, X-Ray

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Integration of virtual screening and susceptibility test to discover active-site subpocket-specific biogenic inhibitors of Helicobacter pylori shikimate dehydrogenase.

International microbiology : the official journal of the Spanish Society for Microbiology 30810934
Shikimate dehydrogenase (HpSDH) (EC 1.1.1.25) is a key enzyme in the shikimate pathway of Helicobacter pylori (H. pylori), which catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. Targeting HpSDH has been recognize...
Alcohol Oxidoreductases Anti-Bacterial Agents Catalytic Domain Computational Biology Crystallography, X-Ray Drug Evaluation, Preclinical Enzyme Inhibitors Helicobacter pylori Microbial Sensitivity Tests Molecular Docking Simulation Protein Conformation
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Classification of crystallization outcomes using deep convolutional neural networks.

PloS one 29924841
The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algori...
Algorithms Crystallization Crystallography, X-Ray Datasets as Topic Image Processing, Computer-Assisted Neural Networks, Computer
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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife 29927385
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
Amino Acid Sequence Animals Binding Sites Crystallography, X-Ray Gene Expression Humans Kinetics Machine Learning Models, Molecular Point Mutation Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Engineering Protein Interaction Domains and Motifs Protein Stability Receptor, Serotonin, 5-HT2C Sequence Alignment Sequence Homology, Amino Acid Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists Thermodynamics
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Insight Analysis of Promiscuous Estrogen Receptor α-Ligand Binding by a Novel Machine Learning Scheme.

Chemical research in toxicology 30019586
Estrogen receptor α (ERα) plays a significant role in occurrence of breast cancer and may cause various adverse side-effects when ERα is an off-target protein. A theoretical model was derived to predict the binding affinity of ERα using the pharmacop...
Computer Simulation Crystallography, X-Ray Estrogen Receptor alpha Humans Ligands Machine Learning Models, Molecular Protein Binding Protein Conformation Quantitative Structure-Activity Relationship Reproducibility of Results Support Vector Machine
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Enhancing fluorescent protein photostability through robot-assisted photobleaching.

Integrative biology : quantitative biosciences from nano to macro 29897363
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...
Bacterial Proteins Crystallography, X-Ray Escherichia coli HeLa Cells Humans Light Luminescent Proteins Models, Biological Mutation Photobleaching Photochemistry Plasmids Robotics
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Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges.

Journal of computer-aided molecular design 30116918
Advanced mathematics, such as multiscale weighted colored subgraph and element specific persistent homology, and machine learning including deep neural networks were integrated to construct mathematical deep learning models for pose and binding affin...
Binding Sites Cathepsins Computer-Aided Design Crystallography, X-Ray Databases, Protein Deep Learning Drug Design Ligands Molecular Docking Simulation Protein Binding Protein Conformation Protein Kinases Receptors, Cytoplasmic and Nuclear Thermodynamics
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General Method for the Identification of Crystal Faces Using Raman Spectroscopy Combined with Machine Learning and Application to the Epitaxial Growth of Acetaminophen.

Langmuir : the ACS journal of surfaces and colloids 30053784
Crystal morphology is one of the key crystallographic characteristics that governs the macroscopic properties of crystalline materials. The identification of crystal faces, or face indexing, is an important technique that is used to get information r...
Acetaminophen Algorithms Crystallization Crystallography, X-Ray Galactose Machine Learning Mannitol Spectrum Analysis, Raman X-Ray Diffraction Xylitol
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Blind prediction of protein B-factor and flexibility.

The Journal of chemical physics 30292224
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...
Algorithms Animals Computer Graphics Crystallography, X-Ray Databases, Protein Elasticity Humans Machine Learning Protein Conformation Receptors, Fc
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A combined drug discovery strategy based on machine learning and molecular docking.

Chemical biology & drug design 30688405
Data mining methods based on machine learning play an increasingly important role in drug design and discovery. In the current work, eight machine learning methods including decision trees, k-Nearest neighbor, support vector machines, random forests,...
Area Under Curve Binding Sites Crystallography, X-Ray Databases, Factual Drug Discovery Inhibitory Concentration 50 Machine Learning Molecular Docking Simulation Principal Component Analysis Protein Structure, Tertiary ROC Curve
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mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research 31114883
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...
Benchmarking Binding Sites Crystallography, X-Ray Datasets as Topic Humans Internet Machine Learning Mutation, Missense Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Domains and Motifs Protein Interaction Mapping Proteins Software Thermodynamics
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