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Models, Molecular

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CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes.

BMC bioinformatics Dec 28, 2017
BACKGROUND: The β-Lactamase (BL) enzyme family is an important class of enzymes that plays a key role in bacterial resistance to antibiotics. As the newly identified number of BL enzymes is increasing daily, it is imperative to develop a computationa...
ROC Curve Databases, Protein Models, Molecular Amino Acid Sequence Neural Networks, Computer Algorithms Reproducibility of Results beta-Lactamases
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A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction.

BMC bioinformatics Dec 28, 2017
BACKGROUND: Direct prediction of the three-dimensional (3D) structures of proteins from one-dimensional (1D) sequences is a challenging problem. Significant structural characteristics such as solvent accessibility and contact number are essential for...
Algorithms Proteins Models, Molecular Solvents Neural Networks, Computer Machine Learning
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Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks.

Cell systems Dec 20, 2017
While genes are defined by sequence, in biological systems a protein's function is largely determined by its three-dimensional structure. Evolutionary information embedded within multiple sequence alignments provides a rich source of data for inferri...
Proteins Databases, Protein Models, Molecular Humans Animals Algorithms Probability Neural Networks, Computer Forecasting Computational Biology Protein Folding Protein Conformation Machine Learning Sequence Alignment
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Physicochemical characterization and in vitro hypoglycemic activities of polysaccharides from Sargassum pallidum by microwave-assisted aqueous two-phase extraction.

International journal of biological macromolecules Dec 19, 2017
Microwave-assisted aqueous two-phase extraction (MAATPE) was applied for simultaneous extraction and separation of polysaccharides from Sargassum pallidum (SPPs). The optimal extraction parameters, physicochemical properties, and hypoglycemic activit...
Models, Molecular Polysaccharides Liquid-Liquid Extraction Molecular Weight Cell Line, Tumor Hypoglycemic Agents Amylases Spectroscopy, Fourier Transform Infrared Humans Sargassum Microwaves Monosaccharides Molecular Conformation alpha-Glucosidases Microscopy, Atomic Force Glycoside Hydrolase Inhibitors Chemical Phenomena
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In silico toxicity profiling of natural product compound libraries from African flora with anti-malarial and anti-HIV properties.

Computational biology and chemistry Dec 6, 2017
This paper describes an analysis of the diversity and chemical toxicity assessment of three chemical libraries of compounds from African flora (the p-ANAPL, AfroMalariaDb, and Afro-HIV), respectively containing compounds exhibiting activities against...
Principal Component Analysis Models, Molecular Molecular Structure Mutagens Maximum Tolerated Dose Antimalarials Datasets as Topic Machine Learning Computer Simulation Africa Anti-HIV Agents Humans Small Molecule Libraries
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Protein structure modeling and refinement by global optimization in CASP12.

Proteins Dec 5, 2017
For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequ...
Computational Biology Support Vector Machine Models, Statistical Proteins Humans Machine Learning Algorithms Protein Conformation Protein Folding Sequence Analysis, Protein Protein Interaction Domains and Motifs Models, Molecular Molecular Dynamics Simulation Crystallography, X-Ray
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Assessment of the model refinement category in CASP12.

Proteins Nov 29, 2017
We here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the pre...
Computational Biology Proteins Models, Molecular Protein Folding Sequence Analysis, Protein Humans Crystallography, X-Ray Machine Learning Protein Conformation Algorithms
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Design of a calix[4]arene-functionalized metal-organic framework probe for highly sensitive and selective monitor of hippuric acid for indexing toluene exposure.

Analytica chimica acta Nov 23, 2017
In the present work, a novel metal-organic framework (MOF) fluorescent probe was prepared by post-synthetic modification of MIL-53-NH(Al) with carboxylatocalix[4]arene (CC[4]A). The introduced CC[4]A could not only enhance the fluorescence performanc...
Metal-Organic Frameworks Models, Molecular Urinalysis Humans Fluorescent Dyes Reagent Strips Toluene Phenols Limit of Detection Spectrometry, Fluorescence Calixarenes Hippurates
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B-factor profile prediction for RNA flexibility using support vector machines.

Journal of computational chemistry Nov 21, 2017
Determining the flexibility of structured biomolecules is important for understanding their biological functions. One quantitative measurement of flexibility is the atomic Debye-Waller factor or temperature B-factor. Most existing studies are limited...
Models, Molecular RNA, Ribosomal Temperature Support Vector Machine
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Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.

Proteins Nov 14, 2017
We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successf...
Protein Folding Sequence Alignment Sequence Analysis, Protein Algorithms Humans Computational Biology Crystallography, X-Ray Machine Learning Databases, Protein Proteins Protein Conformation Models, Molecular
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