AIMC Topic: Proteins

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Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

Journal of structural and functional genomics Jan 12, 2017
Protein database search for public databases is a fundamental step in the target selection of proteins in structural and functional genomics and also for inferring protein structure, function, and evolution. Most database search methods employ amino ...
Sequence Alignment Sequence Analysis, Protein Computer Heuristics Proteins Databases, Protein Models, Molecular Algorithms Computational Biology
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Automatic query generation using word embeddings for retrieving passages describing experimental methods.

Database : the journal of biological databases and curation Jan 10, 2017
Information regarding the physical interactions among proteins is crucial, since protein-protein interactions (PPIs) are central for many biological processes. The experimental techniques used to verify PPIs are vital for characterizing and assessing...
Biological Ontologies Data Curation Proteins Databases, Protein Data Mining
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Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.

PLoS computational biology Jan 5, 2017
MOTIVATION: Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predict...
Proteins Neural Networks, Computer Databases, Protein Protein Conformation Sequence Analysis, Protein Machine Learning Algorithms Computational Biology
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Toward amino acid typing for proteins in FFLUX.

Journal of computational chemistry Dec 19, 2016
Continuing the development of the FFLUX, a multipolar polarizable force field driven by machine learning, we present a modern approach to atom-typing and building transferable models for predicting atomic properties in proteins. Amino acid atomic cha...
Molecular Structure Amino Acids Quantum Theory Machine Learning Computational Biology Proteins
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Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility.

Proteins Dec 5, 2016
Predicting protein conformational changes from unbound structures or even homology models to bound structures remains a critical challenge for protein docking. Here we present a study directly addressing the challenge by reducing the dimensionality a...
Machine Learning Software Benchmarking Protein Conformation Computational Biology Research Design Binding Sites Dimensional Measurement Accuracy Molecular Docking Simulation Models, Statistical Protein Multimerization Thermodynamics Protein Binding Proteins Structural Homology, Protein
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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...
Neural Networks, Computer Machine Learning Algorithms Data Accuracy Protein Structure, Tertiary Support Vector Machine Proteins Models, Molecular
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Microwave-assisted grafting polymerization modification of nylon 6 capillary-channeled polymer fibers for enhanced weak cation exchange protein separations.

Analytica chimica acta Dec 3, 2016
A weak cation exchange liquid chromatography stationary phase (nylon-COOH) was prepared by grafting polyacrylic acid on to native nylon 6 capillary-channeled polymer (C-CP) fibers via a microwave-assisted radical polymerization. To the best of our kn...
Antiporters Caprolactam Reproducibility of Results Microwaves Proteins Polymerization Polymers Chromatography, Ion Exchange
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Boosting Docking-Based Virtual Screening with Deep Learning.

Journal of chemical information and modeling Nov 29, 2016
In this work, we propose a deep learning approach to improve docking-based virtual screening. The deep neural network that is introduced, DeepVS, uses the output of a docking program and learns how to extract relevant features from basic data such as...
ROC Curve Humans Proteins Molecular Docking Simulation Ligands Computer-Aided Design Neural Networks, Computer Drug Design Software Algorithms
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A Graph Approach to Mining Biological Patterns in the Binding Interfaces.

Journal of computational biology : a journal of computational molecular cell biology Nov 28, 2016
Protein-RNA interactions play important roles in the biological systems. Searching for regular patterns in the Protein-RNA binding interfaces is important for understanding how protein and RNA recognize each other and bind to form a complex. Herein, ...
Amino Acid Motifs Protein Interaction Domains and Motifs Protein Binding Protein Conformation Computational Biology Proteins Binding Sites RNA-Binding Proteins Data Mining Computer Graphics Support Vector Machine RNA Humans Animals Molecular Docking Simulation
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Prediction of Protein-Protein Interactions by Evidence Combining Methods.

International journal of molecular sciences Nov 22, 2016
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of c...
Humans Arabidopsis Mice Computational Biology Computer Simulation Animals Datasets as Topic Saccharomyces cerevisiae Drosophila melanogaster Models, Molecular Support Vector Machine Protein Interaction Mapping Data Mining Escherichia coli Protein Interaction Domains and Motifs Molecular Sequence Annotation High-Throughput Nucleotide Sequencing Proteins Gene Ontology
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