AIMC Topic: Position-Specific Scoring Matrices

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Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods.

BMC bioinformatics Dec 1, 2017
BACKGROUND: Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human sp...
Humans Machine Learning RNA Splicing Genome, Human Exons Introns Computational Biology Position-Specific Scoring Matrices Nucleotide Motifs Base Sequence
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Prediction of protein subcellular localization with oversampling approach and Chou's general PseAAC.

Journal of theoretical biology Oct 31, 2017
Predicting protein subcellular location with support vector machine has been a popular research area recently because of the dramatic explosion of bioinformation. Though substantial achievements have been obtained, few researchers considered the prob...
Proteins Databases, Protein Principal Component Analysis Computational Biology Support Vector Machine Position-Specific Scoring Matrices Amino Acids Protein Transport Algorithms
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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...
Bacterial Proteins Amino Acid Sequence Position-Specific Scoring Matrices Mycobacterium Computational Biology Membrane Proteins Evolution, Molecular Artificial Intelligence
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EMQIT: a machine learning approach for energy based PWM matrix quality improvement.

Biology direct Aug 1, 2017
BACKGROUND: Transcription factor binding affinities to DNA play a key role for the gene regulation. Learning the specificity of the mechanisms of binding TFs to DNA is important both to experimentalists and theoreticians. With the development of high...
Transcription Factors Position-Specific Scoring Matrices Models, Molecular Gene Expression Regulation Binding Sites ROC Curve Datasets as Topic Computational Biology Models, Genetic Machine Learning Software
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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...
Amino Acids Amino Acid Sequence Lysine Position-Specific Scoring Matrices Acetylation Computational Biology Support Vector Machine Protein Processing, Post-Translational Reproducibility of Results Peptides Algorithms
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Detrended cross-correlation coefficient: Application to predict apoptosis protein subcellular localization.

Mathematical biosciences Oct 6, 2016
Apoptosis, or programed cell death, plays a central role in the development and homeostasis of an organism. Obtaining information on subcellular location of apoptosis proteins is very helpful for understanding the apoptosis mechanism. The prediction ...
Models, Theoretical Apoptosis Regulatory Proteins Position-Specific Scoring Matrices Support Vector Machine Apoptosis
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Identification of Multi-Functional Enzyme with Multi-Label Classifier.

PloS one Apr 14, 2016
Enzymes are important and effective biological catalyst proteins participating in almost all active cell processes. Identification of multi-functional enzymes is essential in understanding the function of enzymes. Machine learning methods perform bet...
Position-Specific Scoring Matrices Humans Multifunctional Enzymes Machine Learning Algorithms Animals
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MATEPRED-A-SVM-Based Prediction Method for Multidrug And Toxin Extrusion (MATE) Proteins.

Computational biology and chemistry Jul 29, 2015
The growth and spread of drug resistance in bacteria have been well established in both mankind and beasts and thus is a serious public health concern. Due to the increasing problem of drug resistance, control of infectious diseases like diarrhea, pn...
Drug Resistance Organic Cation Transport Proteins Position-Specific Scoring Matrices Amino Acids Reproducibility of Results Dipeptides Support Vector Machine Hydrophobic and Hydrophilic Interactions
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A Deep Learning and PSSM Profile Approach for Accurate SNARE Protein Prediction.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2025
SNARE proteins play a pivotal role in membrane fusion and various cellular processes. Accurate identification of SNARE proteins is crucial for elucidating their functions in both health and disease contexts. This chapter presents a novel approach emp...
Humans Databases, Protein Position-Specific Scoring Matrices SNARE Proteins Deep Learning Computational Biology Neural Networks, Computer
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ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
Deep neural networks have demonstrated improved performance at predicting sequence specificities of DNA- and RNA-binding proteins. However, it remains unclear why they perform better than previous methods that rely on k-mers and position weight matri...
RNA Position-Specific Scoring Matrices RNA-Binding Proteins DNA Neural Networks, Computer Protein Binding
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