ArticleJournal of theoretical biology2009
Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices.
Article in Journal of theoretical biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Graph Theory-Based Sequence Descriptors as Remote Homology Predictors.Biomolecules · 2019Article
- Carbon Nanotubes' Effect on Mitochondrial Oxygen Flux Dynamics: Polarography Experimental Study and Machine Learning Models using Star Graph Trace Invariants of Raman Spectra.Nanomaterials (Basel, Switzerland) · 2017Article
- MultiP-Apo: A Multilabel Predictor for Identifying Subcellular Locations of Apoptosis Proteins.Computational intelligence and neuroscience · 2017Article
- In silico study of rotavirus VP7 surface accessible conserved regions for antiviral drug/vaccine design.PloS one · 2012Article
- Fragment-based optimization of small molecule CXCL12 inhibitors for antagonizing the CXCL12/CXCR4 interaction.Current topics in medicinal chemistry · 2012Article
- An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference.PloS one · 2011Article
- Analysis of protein pathway networks using hybrid properties.Molecules (Basel, Switzerland) · 2010Article
- Prediction of subcellular location of mycobacterial protein using feature selection techniques.Molecular diversity · 2010Article
- Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis.Nucleic acids research · 2010Article
- Scoring function for DNA-drug docking of anticancer and antiparasitic compounds based on spectral moments of 2D lattice graphs for molecular dynamics trajectories.European journal of medicinal chemistry · 2009Article
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6 authors.
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Abstract
The importance of the promoter sequences in the function regulation of several important mycobacterial pathogens creates the necessity to design simple and fast theoretical models that can predict them. This work proposes two DNA promoter QSAR models based on pseudo-folding lattice network (LN) and star-graphs (SG) topological indices. In addition, a comparative study with the previous RNA electrostatic parameters of thermodynamically-driven secondary structure folding representations has been carried out. The best model of this work was obtained with only two LN stochastic electrostatic potentials and it is characterized by accuracy, selectivity and specificity of 90.87%, 82.96% and 92.95%, respectively. In addition, we pointed out the SG result dependence on the DNA sequence codification and we proposed a QSAR model based on codons and only three SG spectral moments.
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