AIMC Topic: Sequence Analysis, Protein

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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...
Software Databases, Protein Cysteine Sequence Analysis, Protein Support Vector Machine Protein Processing, Post-Translational
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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 ...
Sequence Homology, Amino Acid Sequence Analysis, Protein Principal Component Analysis Amino Acid Sequence Protein Conformation Protein Folding Datasets as Topic Machine Learning Computational Biology
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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...
Computational Biology Sequence Analysis, Protein Protein Interaction Domains and Motifs Support Vector Machine Internet Amino Acid Sequence Software Benchmarking Proteins Protein Interaction Mapping Molecular Docking Simulation
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predCar-site: Carbonylation sites prediction in proteins using support vector machine with resolving data imbalanced issue.

Analytical biochemistry Mar 9, 2017
The carbonylation is found as an irreversible post-translational modification and considered a biomarker of oxidative stress. It plays major role not only in orchestrating various biological processes but also associated with some diseases such as Al...
Humans Software Algorithms Protein Processing, Post-Translational Proteins Models, Biological Computational Biology Support Vector Machine Protein Carbonylation Sequence Analysis, Protein
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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 ...
Algorithms Proteins Databases, Protein Computational Biology Sequence Analysis, Protein Models, Molecular Sequence Alignment Computer Heuristics
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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...
Protein Conformation Sequence Analysis, Protein Machine Learning Algorithms Proteins Databases, Protein Computational Biology Neural Networks, Computer
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Combining sequence and Gene Ontology for protein module detection in the Weighted Network.

Journal of theoretical biology Oct 29, 2016
Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating ...
Sequence Analysis, Protein Proteins Gene Ontology
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RAFP-Pred: Robust Prediction of Antifreeze Proteins Using Localized Analysis of n-Peptide Compositions.

IEEE/ACM transactions on computational biology and bioinformatics Oct 13, 2016
In extreme cold weather, living organisms produce Antifreeze Proteins (AFPs) to counter the otherwise lethal intracellular formation of ice. Structures and sequences of various AFPs exhibit a high degree of heterogeneity, consequently the prediction ...
Machine Learning Sequence Analysis, Protein Antifreeze Proteins Computational Biology Databases, Protein Dipeptides Algorithms ROC Curve
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ASAP: a machine learning framework for local protein properties.

Database : the journal of biological databases and curation Oct 2, 2016
Determining residue-level protein properties, such as sites of post-translational modifications (PTMs), is vital to understanding protein function. Experimental methods are costly and time-consuming, while traditional rule-based computational methods...
Sequence Analysis, Protein Internet Machine Learning Molecular Sequence Annotation Peptides
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Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences.

BioMed research international May 23, 2016
We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM) model and Local Phase Quantization (LPQ) to predict PPIs from protein sequences. The main improvements are the results of representing protein s...
Sequence Analysis, Protein Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Humans Databases, Protein Predictive Value of Tests Support Vector Machine
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