AIMC Topic: Sequence Analysis, Protein

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Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.

Proteins Oct 26, 2017
Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted resid...
Algorithms Computational Biology Proteins Humans Machine Learning Protein Conformation Sequence Analysis, Protein Protein Interaction Domains and Motifs Models, Molecular Molecular Dynamics Simulation Crystallography, X-Ray
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Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization.

PLoS computational biology Oct 23, 2017
There is growing interest in studying and engineering integral membrane proteins (MPs) that play key roles in sensing and regulating cellular response to diverse external signals. A MP must be expressed, correctly inserted and folded in a lipid bilay...
Cell Membrane Lipid Bilayers Sequence Analysis, Protein Ion Channels Subcellular Fractions Rhodopsin Drug Design Structure-Activity Relationship HEK293 Cells Humans Machine Learning
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A Computational-Based Method for Predicting Drug-Target Interactions by Using Stacked Autoencoder Deep Neural Network.

Journal of computational biology : a journal of computational molecular cell biology Sep 11, 2017
Identifying the interaction between drugs and target proteins is an important area of drug research, which provides a broad prospect for low-risk and faster drug development. However, due to the limitations of traditional experiments when revealing d...
Protein Binding Databases, Chemical Sequence Analysis, Protein Reproducibility of Results Molecular Docking Simulation Deep Learning
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Prediction of N-linked glycosylation sites using position relative features and statistical moments.

PloS one Aug 10, 2017
Glycosylation is one of the most complex post translation modification in eukaryotic cells. Almost 50% of the human proteome is glycosylated as glycosylation plays a vital role in various biological functions such as antigen's recognition, cell-cell ...
Support Vector Machine Databases, Protein Amino Acid Sequence Sequence Analysis, Protein Humans Algorithms Neural Networks, Computer Computational Biology Glycosylation
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Protein binding hot spots prediction from sequence only by a new ensemble learning method.

Amino acids Aug 1, 2017
UNLABELLED: Hot spots are interfacial core areas of binding proteins, which have been applied as targets in drug design. Experimental methods are costly in both time and expense to locate hot spot areas. Recently, in-silicon computational methods hav...
Databases, Protein Models, Molecular Sequence Analysis, Protein Machine Learning Algorithms
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A novel alignment-free method to classify protein folding types by combining spectral graph clustering with Chou's pseudo amino acid composition.

Journal of theoretical biology May 3, 2017
The present work employs pseudo amino acid composition (PseAAC) for encoding the protein sequences in their numeric form. Later this will be arranged in the similarity matrix, which serves as input for spectral graph clustering method. Spectral metho...
Algorithms Proteins Protein Folding Sequence Alignment Sequence Analysis, Protein Machine Learning
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Investigating Correlation between Protein Sequence Similarity and Semantic Similarity Using Gene Ontology Annotations.

IEEE/ACM transactions on computational biology and bioinformatics Apr 18, 2017
Sequence similarity is a commonly used measure to compare proteins. With the increasing use of ontologies, semantic (function) similarity is getting importance. The correlation between these measures has been applied in the evaluation of new semantic...
Humans Animals Mice Molecular Sequence Annotation Gene Ontology Sequence Alignment Sequence Analysis, Protein Databases, Protein Amino Acid Sequence Semantics Computational Biology Proteins
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S-SulfPred: A sensitive predictor to capture S-sulfenylation sites based on a resampling one-sided selection undersampling-synthetic minority oversampling technique.

Journal of theoretical biology Apr 12, 2017
Protein S-sulfenylation is a reversible post-translational modification involving covalent attachment of hydroxide to the thiol group of cysteine residues, which is involved in various biological processes including cell signaling, response to stress...
Cysteine Sequence Analysis, Protein Protein Processing, Post-Translational Databases, Protein Software Support Vector Machine
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Extracting features from protein sequences to improve deep extreme learning machine for protein fold recognition.

Journal of theoretical biology Mar 27, 2017
Protein fold recognition is an important problem in bioinformatics to predict three-dimensional structure of a protein. One of the most challenging tasks in protein fold recognition problem is the extraction of efficient features from the amino-acid ...
Amino Acid Sequence Datasets as Topic Protein Conformation Machine Learning Computational Biology Protein Folding Principal Component Analysis Sequence Homology, Amino Acid Sequence Analysis, Protein
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InterPred: A pipeline to identify and model protein-protein interactions.

Proteins Mar 21, 2017
Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the numb...
Protein Interaction Mapping Sequence Analysis, Protein Protein Interaction Domains and Motifs Internet Benchmarking Amino Acid Sequence Support Vector Machine Proteins Software Molecular Docking Simulation Computational Biology
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