AIMC Topic: Protein Structure, Tertiary

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DESTINI: A deep-learning approach to contact-driven protein structure prediction.

Scientific reports Mar 5, 2019
The amino acid sequence of a protein encodes the blueprint of its native structure. To predict the corresponding structural fold from the protein's sequence is one of most challenging problems in computational biology. In this work, we introduce DEST...
Computational Biology Proteins Protein Structure, Tertiary Deep Learning
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DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure.

PloS one Jan 8, 2019
Rapid, accurate prediction of protein structure from amino acid sequence would accelerate fields as diverse as drug discovery, synthetic biology and disease diagnosis. Massively improved prediction of protein structures has been driven by improving t...
Databases, Protein Models, Molecular Amino Acid Sequence Computational Biology Support Vector Machine Proteins Protein Structure, Tertiary Sequence Analysis, Protein Algorithms Deep Learning
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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...
Proteins Models, Molecular Protein Structure, Tertiary Computer Heuristics Software Algorithms Computational Biology
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Development of machine learning models to predict inhibition of 3-dehydroquinate dehydratase.

Chemical biology & drug design May 18, 2018
In this study, we describe the development of new machine learning models to predict inhibition of the enzyme 3-dehydroquinate dehydratase (DHQD). This enzyme is the third step of the shikimate pathway and is responsible for the synthesis of chorisma...
Hydro-Lyases Shikimic Acid Static Electricity Binding Sites Protein Structure, Tertiary Molecular Docking Simulation ROC Curve Area Under Curve Humans Machine Learning
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RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning.

BMC bioinformatics May 8, 2018
BACKGROUND: Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding protein tertiary...
Software Deep Learning Cluster Analysis Proteins Databases, Protein Amino Acids Costs and Cost Analysis Entropy Protein Structure, Tertiary
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Recent Progress in Machine Learning-Based Methods for Protein Fold Recognition.

International journal of molecular sciences Dec 16, 2016
Knowledge on protein folding has a profound impact on understanding the heterogeneity and molecular function of proteins, further facilitating drug design. Predicting the 3D structure (fold) of a protein is a key problem in molecular biology. Determi...
Computational Biology Protein Folding Protein Structure, Tertiary Humans Machine Learning Drug Design
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DeepQA: improving the estimation of single protein model quality with deep belief networks.

BMC bioinformatics Dec 5, 2016
BACKGROUND: Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, w...
Models, Molecular Data Accuracy Protein Structure, Tertiary Support Vector Machine Proteins Neural Networks, Computer Machine Learning Algorithms
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OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method.

Journal of computational biology : a journal of computational molecular cell biology Aug 11, 2016
In the two transmembrane protein types, outer membrane proteins (OMPs) perform diverse important biochemical functions, including substrate transport and passive nutrient uptake and intake. Hence their 3D structures are expected to reveal these funct...
Databases, Protein Biological Transport Bacterial Outer Membrane Proteins Membrane Lipids Protein Structure, Tertiary Protein Interaction Domains and Motifs Support Vector Machine Protein Conformation, alpha-Helical Protein Conformation, beta-Strand
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Antileishmanial activity of novel indolyl-coumarin hybrids: Design, synthesis, biological evaluation, molecular docking study and in silico ADME prediction.

Bioorganic & medicinal chemistry letters Dec 24, 2015
In present work we have designed and synthesized total twelve novel 3-(3-(1H-indol-3-yl)-3-phenylpropanoyl)-4-hydroxy-2H-chromen-2-one derivatives 13(a-l) using Ho(3+) doped CoFe2O4 nanoparticles as catalyst and evaluated for their potential antileis...
Leishmania Oxidoreductases Protein Structure, Tertiary Coumarins Binding Sites Structure-Activity Relationship HeLa Cells Inhibitory Concentration 50 Enzyme Inhibitors Antiprotozoal Agents Protozoan Proteins Drug Design Antioxidants Cell Survival Humans Molecular Docking Simulation
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Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes.

BMC bioinformatics Dec 9, 2015
BACKGROUND: Protein-protein interactions (PPIs) are involved in various biological processes, and underlying mechanism of the interactions plays a crucial role in therapeutics and protein engineering. Most machine learning approaches have been develo...
Protein Structure, Tertiary Dimerization Area Under Curve Hydrogen Bonding Support Vector Machine Proteins Principal Component Analysis ROC Curve Protein Interaction Maps Protein Binding
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