RT Book,_Section
T1 QSAR Study for Macromolecular RNA Folded Secondary Structures of Mycobacterial Promoters with Low Sequence Homology
A1 González Díaz, Humberto
A1 Pérez Bello, Alcides
A1 Uriarte Villares, Eugenio
A1 González Díaz, Yenny
K1 QSAR
K1 RNA secondary structure
K1 Sequence homology
K1 Markov model
K1 Mycobacterial promoters
K1 Electrostatic potential
AB The general belief is that quantitative structure-activity relationships (QSAR) techniques work only for small molecules and, proteins sequences or, more recently, DNA sequences. However, with non-branched graph for proteins and DNA sequences the QSAR often have to be based on powerful non-linear techniques such as support vector machines. In our opinion linear QSAR models based in RNA could be useful to assign biological activity when alignment techniques fail due to low sequence homology. The idea bases in the high level of branching for the RNA graph. This work introduces the so called Markov electrostatic potentials k?M as a new class of RNA 2D-structure descriptors. Subsequently, we validate these molecular descriptors solving a QSAR classification problem for mycobacterial promoter sequences (mps), which constitute a very low sequence homology problem. The model developed (mps = –4.664·0cM + 0.991·1cM – 2.432) was intended to predict whether a naturally occurring sequence is an mps or not on the basis of the calculated kcM value for the corresponding RNA secondary structure. The RNAQSAR approach recognises 115/135 mps (85.2%) and 100% of control sequences. Average predictability and robustness were greater than 95%. A previous non-linear model predicts mps with slightly higher accuracy (97%) but uses a very large parameter space for DNA sequences. Conversely, the kcM-based RNA-QSAR encodes more structural information and needs only two variables
PB MDPI
SN 3-906980-16-2
YR 2005
FD 2005
LK http://hdl.handle.net/10347/26888
UL http://hdl.handle.net/10347/26888
LA eng
NO Proceedings of the 9th International Electronic Conference on Synthetic Organic Chemistry, 1–30 November 2005, MDPI: Basel, Switzerland, doi:10.3390/ecsoc-9-01654
NO The 9th International Electronic Conference on Synthetic Organic Chemistry session Computational Chemistry
NO González-Díaz, H. thanks the Xunta de Galicia (BTF20301PR) for partial financial support
DS Minerva
RD 27 abr 2026