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Models, Molecular

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Gene ontology improves template selection in comparative protein docking.

Proteins Dec 27, 2018
Structural characterization of protein-protein interactions is essential for our ability to study life processes at the molecular level. Computational modeling of protein complexes (protein docking) is important as the source of their structure and a...
Models, Molecular Protein Conformation Gene Ontology Structural Homology, Protein Binding Sites Protein Interaction Mapping Computational Biology Proteins Databases, Protein Molecular Docking Simulation Protein Interaction Maps Protein Binding Humans Software
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Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations.

Proceedings of the National Academy of Sciences of the United States of America Dec 26, 2018
Biophysical interactions between proteins and peptides are key determinants of molecular recognition specificity landscapes. However, an understanding of how molecular structure and residue-level energetics at protein-peptide interfaces shape these l...
Energy Metabolism Drug Resistance, Viral Serine Proteases Peptide Hydrolases Viral Nonstructural Proteins Substrate Specificity Supervised Machine Learning Hepacivirus High-Throughput Nucleotide Sequencing Metabolomics Structure-Activity Relationship Models, Molecular Antiviral Agents
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Rapid and specific detection of Salmonella infections using chemically modified nucleic acid probes.

Analytica chimica acta Dec 21, 2018
Salmonella is a leading source of bacterial foodborne illness in humans, causing gastroenteritis outbreaks with bacteraemia occurrences that can lead to clinical complications and death. Eggs, poultry and pig products are considered as the main carri...
Protein Conformation Salmonella Oligonucleotide Probes Time Factors Deoxyribonucleases Models, Molecular Food Microbiology Nucleic Acid Conformation Limit of Detection Food Safety
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De Novo Molecule Design by Translating from Reduced Graphs to SMILES.

Journal of chemical information and modeling Dec 21, 2018
A key component of automated molecular design is the generation of compound ideas for subsequent filtering and assessment. Recently deep learning approaches have been explored as alternatives to traditional de novo molecular design techniques. Deep l...
Models, Molecular Molecular Structure Pharmaceutical Preparations Drug Design Cheminformatics Deep Learning Databases, Pharmaceutical
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An SVM-based method for assessment of transcription factor-DNA complex models.

BMC bioinformatics Dec 21, 2018
BACKGROUND: Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex struc...
Algorithms DNA Models, Molecular Protein Binding Transcription Factors Support Vector Machine
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Converging a Knowledge-Based Scoring Function: DrugScore.

Journal of chemical information and modeling Dec 18, 2018
We present DrugScore, a new version of the knowledge-based scoring function DrugScore, which builds upon the same formalism used to derive DrugScore but exploits a training data set of nearly 40 000 X-ray complex structures, a highly diverse and the,...
Informatics Models, Molecular Knowledge Bases Ligands Drug Design
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Etching reaction-based photoelectrochemical immunoassay of aflatoxin B in foodstuff using cobalt oxyhydroxide nanosheets-coating cadmium sulfide nanoparticles as the signal tags.

Analytica chimica acta Dec 7, 2018
A new split-type photoelectrochemical (PEC) immunosensing platform was designed for sensitive detection of aflatoxin B (AFB) in foodstuffs, coupling with enzymatic hydrolysate-triggered etching reaction of cobalt oxyhydroxide (CoOOH) on cadmium sulfi...
Cadmium Compounds Aflatoxin B1 Photochemical Processes Sulfides Food Contamination Arachis Feasibility Studies Models, Molecular Food Analysis Molecular Conformation Cobalt Nanoparticles Oxides Electrochemistry Immunoassay
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Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network.

Journal of chemical information and modeling Dec 7, 2018
The CRISPR-Cas9 system derived from adaptive immunity in bacteria and archaea has been developed into a powerful tool for genome engineering with wide-ranging applications. Optimizing single-guide RNA (sgRNA) design to improve efficiency of target cl...
Deep Learning Computational Biology Models, Molecular RNA, Guide, CRISPR-Cas Systems CRISPR-Cas Systems Gene Editing Nucleic Acid Conformation
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Hispaglabridin B, a constituent of liquorice identified by a bioinformatics and machine learning approach, relieves protein-energy wasting by inhibiting forkhead box O1.

British journal of pharmacology Dec 4, 2018
BACKGROUND AND PURPOSE: Liquorice is the root of Glycyrrhiza glabra, which is a popular food in Europe and China that has previously shown benefits for skeletal fatigue and nutrient metabolism. However, the mechanism and active ingredients remain lar...
Dose-Response Relationship, Drug Muscle, Skeletal Structure-Activity Relationship Plant Roots Computational Biology Plant Extracts Mice, Inbred C57BL Glycyrrhiza Transcription, Genetic Muscular Atrophy Forkhead Box Protein O1 Models, Molecular Molecular Structure Benzopyrans Male Machine Learning Mice Animals
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iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations.

Proteins Dec 3, 2018
Quantitative evaluation of binding affinity changes upon mutations is crucial for protein engineering and drug design. Machine learning-based methods are gaining increasing momentum in this field. Due to the limited number of experimental data, using...
Machine Learning Protein Binding Computational Biology Thermodynamics Binding, Competitive Proto-Oncogene Proteins c-mdm2 Mutation Protein Domains Tumor Suppressor Protein p53 Evolution, Molecular Proteins Models, Molecular
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