AIMC Topic: Crystallography, X-Ray

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Structure-activity relationship studies of 1-(1'-hydroxyalkyl)rupestonic acid methyl esters against influenza viruses.

Bioorganic & medicinal chemistry letters Jun 6, 2016
A series of 1-(1'-hydroxyalkyl)rupestonic acid methyl esters were synthesized via the condensation of methyl rupestonate with various aldehydes in the presence of LDA. This mixed aldol reaction was highly stereoselective and all the new compounds wer...
Crystallography, X-Ray Structure-Activity Relationship Azulenes Esters Orthomyxoviridae Sesquiterpenes Microbial Sensitivity Tests Antiviral Agents
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Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries.

Journal of chemical information and modeling May 24, 2016
Virtual screening consists of docking libraries of small molecules to a target protein followed by rank-ordering of the resulting structures using scoring functions. The ability of scoring methods to distinguish between actives and inactives depends ...
Protein Kinases Ligands Crystallography, X-Ray Small Molecule Libraries Protein Binding Support Vector Machine Drug Evaluation, Preclinical Molecular Docking Simulation User-Computer Interface
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DisPredict: A Predictor of Disordered Protein Using Optimized RBF Kernel.

PloS one Oct 30, 2015
Intrinsically disordered proteins or, regions perform important biological functions through their dynamic conformations during binding. Thus accurate identification of these disordered regions have significant implications in proper annotation of fu...
Probability Datasets as Topic Intrinsically Disordered Proteins Area Under Curve Amino Acid Sequence Crystallography, X-Ray Protein Structure, Secondary Algorithms ROC Curve Support Vector Machine
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Using support vector machines to improve elemental ion identification in macromolecular crystal structures.

Acta crystallographica. Section D, Biological crystallography Apr 25, 2015
In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific know...
Nickel Calcium Macromolecular Substances Manganese Crystallography, X-Ray Support Vector Machine Algorithms Protein Conformation Models, Molecular Zinc Iron Metals
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PENG: a neural gas-based approach for pharmacophore elucidation. method design, validation, and virtual screening for novel ligands of LTA4H.

Journal of chemical information and modeling Feb 9, 2015
The pharmacophore concept is commonly employed in virtual screening for hit identification. A pharmacophore is generally defined as the three-dimensional arrangement of the structural and physicochemical features of a compound responsible for its aff...
Ligands High-Throughput Screening Assays Enzyme Inhibitors Crystallography, X-Ray Thermodynamics Epoxide Hydrolases Neural Networks, Computer Aminopeptidases Algorithms Humans Models, Molecular Prospective Studies Benchmarking Reproducibility of Results Protein Binding
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MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures.

Nature communications Jul 4, 2025
At sufficiently high resolution, x-ray crystallography and cryogenic electron microscopy are capable of resolving small spherical map features corresponding to either water or ions. Correct classification of these sites provides crucial insight for u...
Deep Learning Ions Crystallography, X-Ray Cryoelectron Microscopy Water Proteins Models, Molecular
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Next generation technologies for protein structure determination: challenges and breakthroughs in plant biology applications.

Journal of plant physiology Jul 1, 2025
Advancements in structural biology have significantly deepened our understanding of plant proteins, which are central to critical biological functions such as photosynthesis, metabolism, signal transduction, and structural architechture. Gaining insi...
Magnetic Resonance Spectroscopy Cryoelectron Microscopy Plant Proteins Crystallography, X-Ray Protein Conformation Mass Spectrometry Plants
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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...
Models, Molecular Ligands Crystallography, X-Ray Cryoelectron Microscopy Drug Design Deep Learning
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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...
Deep Learning Models, Molecular Electrons Software Nucleic Acid Conformation Nucleic Acids Crystallography, X-Ray
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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 ...
Computational Biology Proteins Crystallography, X-Ray Deep Learning Protein Binding Protein Conformation Protein Interaction Mapping Software Molecular Docking Simulation
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