AIMC Topic: Molecular Structure

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The Liver Toxicity Knowledge Base (LKTB) and drug-induced liver injury (DILI) classification for assessment of human liver injury.

Expert review of gastroenterology & hepatology Oct 9, 2017
Drug-induced liver injury (DILI) is challenging for drug development, clinical practice and regulation. The Liver Toxicity Knowledge Base (LTKB) provides essential data for DILI study. Areas covered: The LTKB provided various types of data that can b...
Severity of Illness Index Incidence Hep G2 Cells Liver Humans Animals Databases, Factual Knowledge Bases Toxicology Chemical and Drug Induced Liver Injury Risk Assessment Toxicogenetics Drug Discovery Structure-Activity Relationship Molecular Structure Pharmaceutical Preparations
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Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.

Journal of computer-aided molecular design Sep 18, 2017
We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and ded...
Algorithms Molecular Docking Simulation Drug Design Protein Binding Humans Machine Learning Molecular Structure Knowledge Bases Ligands Protein Conformation Proteins Databases, Protein Structure-Activity Relationship Binding Sites
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Deep learning methods for protein torsion angle prediction.

BMC bioinformatics Sep 18, 2017
BACKGROUND: Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012, it has achieved success in a...
Protein Structure, Secondary Proteins Molecular Structure Neural Networks, Computer Machine Learning
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Identifying novel factor XIIa inhibitors with PCA-GA-SVM developed vHTS models.

European journal of medicinal chemistry Sep 1, 2017
There currently is renewed interest in blood clotting Factor XII as a potential target for thrombosis inhibition. Historically untargeted, there is little drug information with which to start drug candidate searches. Typical high-throughput screening...
Humans Support Vector Machine Molecular Structure Algorithms Dose-Response Relationship, Drug Factor XIIa Structure-Activity Relationship Blood Proteins Principal Component Analysis Models, Molecular
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A new cyclic lipopeptide isolated from Bacillus amyloliquefaciens HAB-2 and safety evaluation.

Pesticide biochemistry and physiology Aug 31, 2017
Bacillus is the most widely studied biocontrol agent and has been extensively used in the development of biopesticides and fungicides. In this study, a new cyclic lipopeptide was isolated from Bacillus amyloliquefaciens HAB-2 by column chromatography...
Teratogens Toxicity Tests, Acute Molecular Structure Embryo, Nonmammalian Colletotrichum Fungicides, Industrial Animals Spectrum Analysis Lipopeptides Bacillus amyloliquefaciens Microbial Sensitivity Tests Zebrafish Chromatography, Liquid Peptides, Cyclic Biological Control Agents
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Bioactivity and structure-activity relationship of cinnamic acid derivatives and its heteroaromatic ring analogues as potential high-efficient acaricides against Psoroptes cuniculi.

Bioorganic & medicinal chemistry letters Aug 24, 2017
A series of cinnamic acid derivatives and its heteroaromatic ring analogues were synthesized and evaluated for acaricidal activity in vitro against Psoroptes cuniculi, a mange mite. Among them, eight compounds showed the higher activity with median l...
Dose-Response Relationship, Drug Structure-Activity Relationship Molecular Structure Cinnamates Animals Acaricides Psoroptidae
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Protein asparagine deamidation prediction based on structures with machine learning methods.

PloS one Jul 21, 2017
Chemical stability is a major concern in the development of protein therapeutics due to its impact on both efficacy and safety. Protein "hotspots" are amino acid residues that are subject to various chemical modifications, including deamidation, isom...
Software Data Mining Computer Simulation Solvents ROC Curve Asparagine Molecular Structure Models, Statistical Supervised Machine Learning Amides
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Detection of lithospermate B in rat plasma at the nanogram level by LC/MS in multi reaction monitoring mode.

Journal of food and drug analysis Jul 8, 2017
Low bioavailability and high binding affinity to plasma proteins led to the difficulty for the quantitative detection of lithospermate B (LSB) in plasma. This study aimed to develop a protocol for detecting LSB in plasma. A method was employed to qua...
Drugs, Chinese Herbal Administration, Oral Biological Availability Mass Spectrometry Animals Chromatography, Liquid Male Molecular Structure Reproducibility of Results Protein Binding Rats
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Rapid characterization of metabolites in soybean using ultra high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) and screening for α-glucosidase inhibitory and antioxidant properties through different solvent systems.

Journal of food and drug analysis Jun 15, 2017
This work was the first to investigate on the simultaneous characterization of metabolite profiles in soybean using UPLC-ESI-Q-TOF-MS/MS. Twenty two compositions were observed within 14 min from the methanol extract and confirmed as twelve isoflavone...
Antioxidants Plant Extracts Metabolomics Molecular Structure Chromatography, High Pressure Liquid Metabolome Phytochemicals Solvents Tandem Mass Spectrometry Glycine max Glycoside Hydrolase Inhibitors Spectrometry, Mass, Electrospray Ionization Isoflavones Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Prediction of Collision Cross-Section Values for Small Molecules: Application to Pesticide Residue Analysis.

Analytical chemistry Jun 7, 2017
The use of collision cross-section (CCS) values obtained by ion mobility high-resolution mass spectrometry has added a third dimension (alongside retention time and exact mass) to aid in the identification of compounds. However, its utility is limite...
Pesticide Residues Small Molecule Libraries Ion Mobility Spectrometry Neural Networks, Computer Mass Spectrometry Molecular Structure
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