AIMC Topic: Models, Molecular

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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...
Transcription Factors Algorithms Support Vector Machine Protein Binding DNA Models, Molecular
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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,...
Drug Design Models, Molecular Knowledge Bases Ligands Informatics
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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...
Photochemical Processes Immunoassay Electrochemistry Food Analysis Aflatoxin B1 Models, Molecular Cobalt Cadmium Compounds Nanoparticles Arachis Oxides Feasibility Studies Sulfides Food Contamination Molecular Conformation
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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...
Gene Editing Nucleic Acid Conformation RNA, Guide, CRISPR-Cas Systems Computational Biology Models, Molecular CRISPR-Cas Systems Deep Learning
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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...
Structure-Activity Relationship Plant Roots Machine Learning Transcription, Genetic Animals Muscular Atrophy Models, Molecular Molecular Structure Mice Forkhead Box Protein O1 Mice, Inbred C57BL Male Benzopyrans Computational Biology Dose-Response Relationship, Drug Glycyrrhiza Plant Extracts Muscle, Skeletal
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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...
Evolution, Molecular Proteins Models, Molecular Machine Learning Protein Binding Computational Biology Thermodynamics Binding, Competitive Proto-Oncogene Proteins c-mdm2 Mutation Protein Domains Tumor Suppressor Protein p53
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BetaDL: A protein beta-sheet predictor utilizing a deep learning model and independent set solution.

Computers in biology and medicine Dec 2, 2018
The sequence-based prediction of beta-residue contacts and beta-sheet structures contain key information for protein structure prediction. However, the determination of beta-sheet structures poses numerous challenges due to long-range beta-residue in...
Databases, Protein Models, Molecular Protein Conformation, beta-Strand Computational Biology Proteins Software Deep Learning
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A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes.

Scientific reports Nov 13, 2018
Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious mutation/screening cycles for the improvement of proteins. Recently, knowledge-based approaches have fac...
Substrate Specificity Aspergillus niger Directed Molecular Evolution Catalytic Domain Machine Learning Epoxide Hydrolases Stereoisomerism Models, Molecular Mutation
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Two New Heuristic Methods for Protein Model Quality Assessment.

IEEE/ACM transactions on computational biology and bioinformatics Nov 9, 2018
Protein tertiary structure prediction is an important open challenge in bioinformatics and requires effective methods to accurately evaluate the quality of protein 3-D models generated computationally. Many quality assessment (QA) methods have been p...
Software Algorithms Computational Biology Proteins Computer Heuristics Models, Molecular Protein Structure, Tertiary
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Dihydropteroate synthase based sensor for screening multi-sulfonamides residue and its comparison with broad-specific antibody based immunoassay by molecular modeling analysis.

Analytica chimica acta Nov 8, 2018
A biosensor that could simultaneously detect multi-analyte as many as in a single test is more favored when facing lots of samples for screening purpose. In such a biosensor, the recognition element with broad specificity and highly affinity is a key...
Animals Sulfonamides Antibodies, Monoclonal Biosensing Techniques Milk Models, Molecular Dihydropteroate Synthase Immunoassay
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