AIMC Topic: Crystallography, X-Ray

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Machine Learning Models for Accurate Prediction of Kinase Inhibitors with Different Binding Modes.

Journal of medicinal chemistry Aug 30, 2019
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 ...
Protein Kinases Datasets as Topic Databases, Chemical Crystallography, X-Ray Machine Learning Protein Binding Protein Kinase Inhibitors
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Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction.

Scientific reports Aug 26, 2019
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...
Computational Biology Crystallography, X-Ray Magnetic Resonance Spectroscopy Protein Structure, Secondary Neural Networks, Computer Algorithms
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Sequence assignment for low-resolution modelling of protein crystal structures.

Acta crystallographica. Section D, Structural biology Jul 31, 2019
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...
Protein Conformation Algorithms Machine Learning Molecular Docking Simulation Proteins Datasets as Topic Software Databases, Protein Crystallography, X-Ray Amino Acid Sequence
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A combined drug discovery strategy based on machine learning and molecular docking.

Chemical biology & drug design Mar 7, 2019
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,...
Molecular Docking Simulation Drug Discovery ROC Curve Principal Component Analysis Machine Learning Databases, Factual Binding Sites Protein Structure, Tertiary Area Under Curve Inhibitory Concentration 50 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 Aug 24, 2018
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...
Enzyme Inhibitors Crystallography, X-Ray Anti-Bacterial Agents Catalytic Domain Protein Conformation Alcohol Oxidoreductases Computational Biology Molecular Docking Simulation Helicobacter pylori Microbial Sensitivity Tests Drug Evaluation, Preclinical
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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 Aug 16, 2018
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...
Protein Conformation Receptors, Cytoplasmic and Nuclear Binding Sites Thermodynamics Cathepsins Protein Kinases Ligands Crystallography, X-Ray Deep Learning Protein Binding Databases, Protein Computer-Aided Design Drug Design Molecular Docking Simulation
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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 Aug 9, 2018
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...
Crystallography, X-Ray Galactose Acetaminophen Mannitol Spectrum Analysis, Raman Crystallization X-Ray Diffraction Xylitol Machine Learning Algorithms
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Insight Analysis of Promiscuous Estrogen Receptor α-Ligand Binding by a Novel Machine Learning Scheme.

Chemical research in toxicology Jul 30, 2018
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...
Humans Quantitative Structure-Activity Relationship Crystallography, X-Ray Protein Conformation Estrogen Receptor alpha Protein Binding Support Vector Machine Models, Molecular Ligands Machine Learning Computer Simulation Reproducibility of Results
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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife Jun 21, 2018
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...
Humans Protein Interaction Domains and Motifs Machine Learning Thermodynamics Protein Conformation, alpha-Helical Point Mutation Crystallography, X-Ray Animals Serotonin 5-HT2 Receptor Antagonists Sequence Alignment Protein Conformation, beta-Strand Sequence Homology, Amino Acid Kinetics Amino Acid Sequence Protein Stability Receptor, Serotonin, 5-HT2C Protein Binding Models, Molecular Gene Expression Serotonin 5-HT2 Receptor Agonists Binding Sites Protein Engineering
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Classification of crystallization outcomes using deep convolutional neural networks.

PloS one Jun 20, 2018
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...
Crystallography, X-Ray Image Processing, Computer-Assisted Neural Networks, Computer Datasets as Topic Crystallization Algorithms
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