AIMC Topic: Protein Binding

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Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction.

BMC bioinformatics Dec 28, 2017
BACKGROUND: Computational scanning of peptide candidates that bind to a specific major histocompatibility complex (MHC) can speed up the peptide-based vaccine development process and therefore various methods are being actively developed. Recently, m...
Humans Machine Learning Reproducibility of Results Internet Alleles Histocompatibility Antigens Class I Amino Acid Sequence Animals Peptides Deep Learning Protein Binding
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New insights into the efficiency of thymol synergistic effect with p-cymene in inhibiting advanced glycation end products: A multi-way analysis based on spectroscopic and electrochemical methods in combination with molecular docking study.

Journal of pharmaceutical and biomedical analysis Dec 24, 2017
Protein glycation in the body is one of the main reasons of diabetes complications. The electrochemical studies on the inhibitory mechanism of glycation are rather scarce. Thus, it is important to investigate the role of electrochemistry in the glyca...
Hypoglycemic Agents Protein Processing, Post-Translational Structure-Activity Relationship Electrochemical Techniques Monoterpenes Arginine Protein Conformation Kinetics Drug Synergism Lysine Serum Albumin, Bovine Glycation End Products, Advanced Molecular Docking Simulation Cymenes Spectrophotometry, Ultraviolet Protein Binding Glycosylation Thymol Binding Sites
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Bionalytical validation study for the determination of unbound ambrisentan in human plasma using rapid equilibrium dialysis followed by ultra performance liquid chromatography coupled to mass spectrometry.

Journal of pharmaceutical and biomedical analysis Dec 16, 2017
Ambrisentan is a highly selective endothelin-1 type A receptor antagonist indicated for use in the treatment of pulmonary hypertension. In this study an assay was developed and validated for the quantification of total and unbound (free) concentratio...
Spectrometry, Mass, Electrospray Ionization Linear Models Calibration Reference Standards Pyridazines Dialysis Phenylpropionates Chromatography, Liquid Antihypertensive Agents Limit of Detection Tandem Mass Spectrometry Humans Reproducibility of Results Protein Binding
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Aptamer facilitated purification of functional proteins.

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences Dec 16, 2017
DNA aptamers are attractive capture probes for affinity chromatography since, in contrast to antibodies, they can be chemically synthesized and, in contrast to tag-specific capture probes (such as Nickel-NTA or Glutathione), they can be used for puri...
MutS DNA Mismatch-Binding Protein Aptamers, Nucleotide Protein Binding Recombinant Proteins Chromatography, Affinity Escherichia coli Electrophoresis, Capillary Electrophoresis, Polyacrylamide Gel Methylation AlkB Enzymes Immobilized Nucleic Acids
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Design, synthesis, antibacterial evaluation and molecular docking studies of some new quinoxaline derivatives targeting dihyropteroate synthase enzyme.

Bioorganic chemistry Dec 5, 2017
Development of new antimicrobial agents is a good solution to overcome drug-resistance problems. From this perspective, new quinoxaline derivatives bearing various bioactive heterocyclic moieties (thiadiazoles, oxadiazoles, pyrazoles and thiazoles) w...
Molecular Structure Hydrophobic and Hydrophilic Interactions Catalytic Domain Gram-Negative Bacteria Drug Design Microbial Sensitivity Tests Protein Binding Structure-Activity Relationship Levofloxacin Yersinia pestis Gram-Positive Bacteria Hydrogen Bonding Dihydropteroate Synthase Quinoxalines Anti-Bacterial Agents Molecular Docking Simulation
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Different protein-protein interface patterns predicted by different machine learning methods.

Scientific reports Nov 22, 2017
Different types of protein-protein interactions make different protein-protein interface patterns. Different machine learning methods are suitable to deal with different types of data. Then, is it the same situation that different interface patterns ...
Machine Learning Algorithms Protein Binding Proteins Analysis of Variance
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A novel peptide/FeO@SiO-Au nanocomposite-based fluorescence biosensor for the highly selective and sensitive detection of prostate-specific antigen.

Talanta Nov 21, 2017
Highly selective and sensitive detection methods are very important for the early diagnosis of prostate-specific antigen (PSA). Here, we present a novel peptide/FeO@SiO-Au nanocomposite-based fluorescence biosensor for highly selective and sensitive ...
Limit of Detection Fluorescence Recovery After Photobleaching Biosensing Techniques Prostate-Specific Antigen Prostate Humans Protein Binding Magnetite Nanoparticles Reproducibility of Results Nanocomposites Fluorescent Dyes Staining and Labeling Male Ferrosoferric Oxide Silicon Dioxide Peptides Fluoresceins
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Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations.

Journal of computer-aided molecular design Nov 13, 2017
We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( https://drugdesigndata.org...
Ligands Protein Conformation Receptors, Cytoplasmic and Nuclear Binding Sites Neural Networks, Computer Computer-Aided Design Machine Learning Drug Design Molecular Docking Simulation Protein Binding Humans Molecular Dynamics Simulation
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Specific chemiluminescent protocol for dual-site recognition of Streptococcus mutans utilizing strong affinity between teicoplanin and Gram-positive bacteria.

Talanta Nov 6, 2017
A novel dual-site recognition protocol was developed for chemiluminescent (CL) detection of Streptococcus mutans (S. mutans) based on a designed antibiotic-affinity strategy. Teicoplanin, a broad-spectrum antibiotic against Gram-positive bacteria, wa...
Iodobenzenes Milk Animals Luminescent Measurements Hydrogen Peroxide Fresh Water Protein Binding Humans Cell Wall Streptococcus mutans Luminol Anti-Bacterial Agents Limit of Detection Saliva Teicoplanin Rats Immunoglobulin G Dipeptides Magnetite Nanoparticles Horseradish Peroxidase Bacterial Proteins
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Specific and intrinsic sequence patterns extracted by deep learning from intra-protein binding and non-binding peptide fragments.

Scientific reports Nov 2, 2017
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins. Here we sh...
Databases, Protein Peptide Fragments Algorithms Amino Acid Sequence Deep Learning Protein Binding Proteins Protein Conformation Binding Sites
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