AIMC Topic: Crystallography, X-Ray

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Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.

Proteins Oct 26, 2017
Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted resid...
Crystallography, X-Ray Protein Conformation Sequence Analysis, Protein Protein Interaction Domains and Motifs Proteins Models, Molecular Molecular Dynamics Simulation Algorithms Computational Biology Humans Machine Learning
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Improved protein contact predictions with the MetaPSICOV2 server in CASP12.

Proteins Sep 29, 2017
In this paper, we present the results for the MetaPSICOV2 contact prediction server in the CASP12 community experiment (http://predictioncenter.org). Over the 35 assessed Free Modelling target domains the MetaPSICOV2 server achieved a mean precision ...
Algorithms Computational Biology Proteins Neural Networks, Computer Machine Learning Software Protein Conformation Protein Interaction Domains and Motifs Models, Molecular Internet Crystallography, X-Ray Humans
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Analysis of deep learning methods for blind protein contact prediction in CASP12.

Proteins Sep 6, 2017
Here we present the results of protein contact prediction achieved in CASP12 by our RaptorX-Contact server, which is an early implementation of our deep learning method for contact prediction. On a set of 38 free-modeling target domains with a median...
Humans Neural Networks, Computer Crystallography, X-Ray Protein Conformation Protein Folding Computational Biology Proteins Models, Molecular Software Algorithms Deep Learning
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Learning the Relationship between the Primary Structure of HIV Envelope Glycoproteins and Neutralization Activity of Particular Antibodies by Using Artificial Neural Networks.

International journal of molecular sciences Oct 11, 2016
The dependency between the primary structure of HIV envelope glycoproteins (ENV) and the neutralization data for given antibodies is very complicated and depends on a large number of factors, such as the binding affinity of a given antibody for a giv...
Antibodies, Neutralizing HIV-1 Inhibitory Concentration 50 HIV Envelope Protein gp120 Crystallography, X-Ray Magnetic Resonance Spectroscopy HIV Infections Databases, Protein Models, Molecular Humans Neural Networks, Computer
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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...
Azulenes Esters Orthomyxoviridae Sesquiterpenes Microbial Sensitivity Tests Crystallography, X-Ray Antiviral Agents Structure-Activity Relationship
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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 ...
User-Computer Interface Small Molecule Libraries Protein Binding Support Vector Machine Ligands Crystallography, X-Ray Drug Evaluation, Preclinical Protein Kinases Molecular Docking Simulation
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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...
Algorithms Area Under Curve ROC Curve Crystallography, X-Ray Amino Acid Sequence Protein Structure, Secondary Support Vector Machine Probability Datasets as Topic Intrinsically Disordered Proteins
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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...
Algorithms Zinc Models, Molecular Iron Metals Support Vector Machine Manganese Crystallography, X-Ray Nickel Protein Conformation Calcium Macromolecular Substances
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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...
Epoxide Hydrolases Enzyme Inhibitors Crystallography, X-Ray Thermodynamics Benchmarking Ligands High-Throughput Screening Assays Humans Reproducibility of Results Neural Networks, Computer Aminopeptidases Protein Binding Algorithms Models, Molecular Prospective Studies
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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...
Crystallography, X-Ray Protein Conformation Magnetic Resonance Spectroscopy Cryoelectron Microscopy Mass Spectrometry Plants Plant Proteins
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