AIMC Topic: Sequence Analysis, Protein

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ProNA2020 predicts protein-DNA, protein-RNA, and protein-protein binding proteins and residues from sequence.

Journal of molecular biology Mar 4, 2020
The intricate details of how proteins bind to proteins, DNA, and RNA are crucial for the understanding of almost all biological processes. Disease-causing sequence variants often affect binding residues. Here, we described a new, comprehensive system...
Protein Binding Computational Biology Proteins DNA Machine Learning Software Animals Binding Sites Eukaryota Sequence Analysis, Protein Prokaryotic Cells RNA Protein Conformation Nucleic Acid Conformation Humans Neural Networks, Computer
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Sequence-Based Prediction of Fuzzy Protein Interactions.

Journal of molecular biology Feb 27, 2020
It is becoming increasingly recognised that disordered proteins may be fuzzy, in that they can exhibit a wide variety of binding modes. In addition to the well-known process of folding upon binding (disorder-to-order transition), many examples are em...
Protein Domains Amino Acid Sequence Intrinsically Disordered Proteins Fuzzy Logic Databases, Protein Models, Molecular Protein Interaction Domains and Motifs Sequence Homology Protein Conformation Protein Folding Sequence Analysis, Protein Algorithms Protein Binding Humans
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Computational Identification and Analysis of Ubiquinone-Binding Proteins.

Cells Feb 24, 2020
Ubiquinone is an important cofactor that plays vital and diverse roles in many biological processes. Ubiquinone-binding proteins (UBPs) are receptor proteins that dock with ubiquinones. Analyzing and identifying UBPs via a computational approach will...
Humans Machine Learning Gene Ontology Binding Sites Sequence Analysis, Protein Protein Interaction Domains and Motifs Position-Specific Scoring Matrices Carrier Proteins Amino Acid Sequence Ubiquinone Protein Binding Computational Biology Membrane Proteins
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Using Weighted Extreme Learning Machine Combined With Scale-Invariant Feature Transform to Predict Protein-Protein Interactions From Protein Evolutionary Information.

IEEE/ACM transactions on computational biology and bioinformatics Jan 10, 2020
Protein-Protein Interactions (PPIs) play an irreplaceable role in biological activities of organisms. Although many high-throughput methods are used to identify PPIs from different kinds of organisms, they have some shortcomings, such as high cost an...
Amino Acid Sequence Protein Interaction Mapping Saccharomyces cerevisiae Proteins Sequence Analysis, Protein Proteins Databases, Protein Helicobacter pylori Protein Interaction Maps Computational Biology Evolution, Molecular Machine Learning Animals Humans
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MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks.

BMC genomics Dec 24, 2019
BACKGROUND: Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database sea...
Proteins Tandem Mass Spectrometry HeLa Cells Sequence Analysis, Protein Neural Networks, Computer Peptides Deep Learning Humans
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NNTox: Gene Ontology-Based Protein Toxicity Prediction Using Neural Network.

Scientific reports Nov 29, 2019
With advancements in synthetic biology, the cost and the time needed for designing and synthesizing customized gene products have been steadily decreasing. Many research laboratories in academia as well as industry routinely create genetically engine...
Sequence Analysis, Protein Toxins, Biological Humans Neural Networks, Computer Proteins Gene Ontology Software Animals
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PSO-LocBact: A Consensus Method for Optimizing Multiple Classifier Results for Predicting the Subcellular Localization of Bacterial Proteins.

BioMed research international Nov 19, 2019
Several computational approaches for predicting subcellular localization have been developed and proposed. These approaches provide diverse performance because of their different combinations of protein features, training datasets, training strategie...
Intracellular Space Computational Biology Bacterial Proteins Sequence Analysis, Protein Machine Learning Algorithms Consensus
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A step-by-step classification algorithm of protein secondary structures based on double-layer SVM model.

Genomics Nov 15, 2019
In this paper, a step-by-step classification algorithm based on double-layer SVM model is constructed to predict the secondary structure of proteins. The most important feature of this algorithm is to improve the prediction accuracy of α+β and α/β cl...
Animals Support Vector Machine Sequence Analysis, Protein Humans Protein Conformation, alpha-Helical Protein Conformation, beta-Strand
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Exploring the limitations of biophysical propensity scales coupled with machine learning for protein sequence analysis.

Scientific reports Nov 15, 2019
Machine learning (ML) is ubiquitous in bioinformatics, due to its versatility. One of the most crucial aspects to consider while training a ML model is to carefully select the optimal feature encoding for the problem at hand. Biophysical propensity s...
Biophysical Phenomena Sequence Analysis, Protein Solvents Propensity Score Cysteine Computational Biology Proteins Oxidation-Reduction Amino Acids Machine Learning
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Novel Descriptors and Digital Signal Processing- Based Method for Protein Sequence Activity Relationship Study.

International journal of molecular sciences Nov 11, 2019
The work aiming to unravel the correlation between protein sequence and function in the absence of structural information can be highly rewarding. We present a new way of considering descriptors from the amino acids index database for modeling and pr...
Machine Learning Tumor Necrosis Factor-alpha Animals Quantitative Structure-Activity Relationship Sequence Analysis, Protein Cytochrome P-450 Enzyme System Catalytic Domain Humans Epoxide Hydrolases Glucagon-Like Peptide-2 Receptor
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