AIMC Topic: Protein Structure, Secondary

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Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics.

PloS one Nov 10, 2015
We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (Gene...
Natural Language Processing Protein Structure, Secondary Support Vector Machine Amino Acid Sequence Nuclear Pore Complex Proteins Proteins Genomics Databases, Protein Computational Biology Proteomics Intrinsically Disordered Proteins
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DisPredict: A Predictor of Disordered Protein Using Optimized RBF Kernel.

PloS one Oct 30, 2015
Intrinsically disordered proteins or, regions perform important biological functions through their dynamic conformations during binding. Thus accurate identification of these disordered regions have significant implications in proper annotation of fu...
Amino Acid Sequence Algorithms Probability Datasets as Topic Intrinsically Disordered Proteins ROC Curve Crystallography, X-Ray Support Vector Machine Protein Structure, Secondary Area Under Curve
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Prediction Enhancement of Residue Real-Value Relative Accessible Surface Area in Transmembrane Helical Proteins by Solving the Output Preference Problem of Machine Learning-Based Predictors.

Journal of chemical information and modeling Oct 20, 2015
The α-helical transmembrane proteins constitute 25% of the entire human proteome space and are difficult targets in high-resolution wet-lab structural studies, calling for accurate computational predictors. We present a novel sequence-based method ca...
Bacterial Proteins Amino Acid Sequence Solubility Membrane Proteins Databases, Protein Machine Learning Models, Chemical Animals Sequence Alignment Humans Protein Structure, Quaternary Solvents Succinate Dehydrogenase Protein Structure, Secondary Wolinella Molecular Sequence Data
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Accurate contact predictions using covariation techniques and machine learning.

Proteins Aug 14, 2015
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effectiv...
Humans Computer Simulation Bacteria Computational Biology Models, Statistical Neural Networks, Computer Machine Learning Software Protein Structure, Secondary Internet Protein Folding Proteins Amino Acid Sequence Sequence Alignment Protein Interaction Domains and Motifs Databases, Protein Viruses Models, Molecular
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Prediction of Peptide and Protein Propensity for Amyloid Formation.

PloS one Aug 4, 2015
Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo str...
Amyloidogenic Proteins Neural Networks, Computer Amyloid Amino Acid Sequence Protein Structure, Secondary
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Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

Scientific reports Jun 22, 2015
Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independentl...
Solvents Protein Structure, Secondary Databases, Protein Models, Molecular Amino Acids Machine Learning Algorithms Proteins
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All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

Proceedings of the National Academy of Sciences of the United States of America Apr 9, 2015
Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-hel...
Receptors, Cell Surface Protein Structure, Tertiary Sequence Analysis, Protein Models, Molecular Escherichia coli Proteins Protein Structure, Secondary Artificial Intelligence Escherichia coli
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Types and effects of protein variations.

Human genetics Jan 24, 2015
Variations in proteins have very large number of diverse effects affecting sequence, structure, stability, interactions, activity, abundance and other properties. Although protein-coding exons cover just over 1 % of the human genome they harbor an di...
Humans Animals Protein Processing, Post-Translational Structure-Activity Relationship Models, Molecular Proteins Databases, Protein Protein Structure, Quaternary Gene Ontology Molecular Dynamics Simulation Protein Structure, Secondary Amino Acid Sequence Protein Folding Genetic Variation
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Prediction of β-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine.

Journal of theoretical biology Oct 22, 2014
β-Lactam class of antibiotics is used as major therapeutic agent against a number of pathogenic microbes. The widespread and indiscriminate use of antibiotics to treat bacterial infection has prompted evolution of several evading mechanisms from the ...
beta-Lactams Anti-Infective Agents Support Vector Machine Protein Structure, Secondary Amino Acid Sequence Sequence Analysis, Protein beta-Lactamases
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A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Aug 7, 2014
Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous metho...
Proteins Databases, Protein Protein Structure, Secondary Neural Networks, Computer Machine Learning
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