AIMC Topic: Amino Acid Sequence

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DRREP: deep ridge regressed epitope predictor.

BMC genomics Oct 3, 2017
INTRODUCTION: The ability to predict epitopes plays an enormous role in vaccine development in terms of our ability to zero in on where to do a more thorough in-vivo analysis of the protein in question. Though for the past decade there have been nume...
Computational Biology Amino Acid Sequence Epitopes, B-Lymphocyte Neural Networks, Computer
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Bi-PSSM: Position specific scoring matrix based intelligent computational model for identification of mycobacterial membrane proteins.

Journal of theoretical biology Sep 18, 2017
Mycobacterium is a pathogenic bacterium, which is a causative agent of tuberculosis (TB) and leprosy. These diseases are very crucial and become the cause of death of millions of people every year in the world. So, the characterize structure of membr...
Evolution, Molecular Bacterial Proteins Amino Acid Sequence Computational Biology Membrane Proteins Artificial Intelligence Mycobacterium Position-Specific Scoring Matrices
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Predicting the helix-helix interactions from correlated residue mutations.

Proteins Aug 24, 2017
Helix-helix interactions are crucial in the structure assembly, stability and function of helix-rich proteins including many membrane proteins. In spite of remarkable progresses over the past decades, the accuracy of predicting protein structures fro...
Membrane Proteins Amino Acid Sequence Binding Sites Machine Learning Protein Binding Computational Biology Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical
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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 Amino Acid Sequence Algorithms Humans Databases, Protein Sequence Analysis, Protein Neural Networks, Computer Computational Biology Glycosylation
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Machine Learning on Signal-to-Noise Ratios Improves Peptide Array Design in SAMDI Mass Spectrometry.

Analytical chemistry Aug 7, 2017
Emerging peptide array technologies are able to profile molecular activities within cell lysates. However, the structural diversity of peptides leads to inherent differences in peptide signal-to-noise ratios (S/N). These complex effects can lead to p...
Amino Acids Amino Acid Sequence Signal-To-Noise Ratio Protein Array Analysis Machine Learning Peptides Mass Spectrometry
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Prediction of lysine propionylation sites using biased SVM and incorporating four different sequence features into Chou's PseAAC.

Journal of molecular graphics & modelling Jul 25, 2017
Lysine propionylation is an important and common protein acylation modification in both prokaryotes and eukaryotes. To better understand the molecular mechanism of propionylation, it is important to identify propionylated substrates and their corresp...
Position-Specific Scoring Matrices Amino Acid Sequence Acetylation Lysine Protein Processing, Post-Translational Amino Acids Algorithms Reproducibility of Results Peptides Computational Biology Support Vector Machine
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Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.

Scientific reports Jul 18, 2017
Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies...
Matrix Metalloproteinases Substrate Specificity Isoenzymes Support Vector Machine Amino Acid Sequence Algorithms Databases, Factual Reproducibility of Results Computational Biology
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Subcellular localization prediction of apoptosis proteins based on evolutionary information and support vector machine.

Artificial intelligence in medicine May 24, 2017
OBJECTIVES: In this paper, a high-quality sequence encoding scheme is proposed for predicting subcellular location of apoptosis proteins.
Computational Biology Support Vector Machine Apoptosis Regulatory Proteins Proteins Apoptosis Evolution, Molecular Databases, Protein Amino Acid Sequence
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Membrane protein contact and structure prediction using co-evolution in conjunction with machine learning.

PloS one May 24, 2017
De novo membrane protein structure prediction is limited to small proteins due to the conformational search space quickly expanding with length. Long-range contacts (24+ amino acid separation)-residue positions distant in sequence, but in close proxi...
Membrane Proteins Models, Molecular Amino Acid Sequence Machine Learning Algorithms Humans Protein Structure, Secondary Protein Folding
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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...
Animals Gene Ontology Mice Sequence Alignment Computational Biology Sequence Analysis, Protein Amino Acid Sequence Humans Proteins Semantics Databases, Protein Molecular Sequence Annotation
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