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2D‐RNA‐coupling numbers: A new computational chemistry approach to link secondary structure topology with biological function
The logistic equation ACO = 23.8 · τ1(2D‐RNA) + 41.4 predicts ACOs with 98.9%, 98.0%, and 97.8% of accuracy in training, leave‐one‐out and 10‐fold cross‐validation, respectively.
3D-chiral quadratic indices of the 'molecular pseudograph's atom adjacency matrix' and their application to central chirality codification: classification of ACE inhibitors and prediction of…
Markovian negentropies in bioinformatics. 1. A picture of footprints after the interaction of the HIV-1 -RNA packaging region with drugs
The entropies of a vibrational Markov chain have been introduced here as physically meaningful descriptors for the local drug-nucleic acid complexes in the interaction of the antibiotic Paromomycin with the packaging region of the RNA present in type-1 HIV.
Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices
- H. Díaz, Y. Pérez-Castillo, G. Podda, E. Uriarte
- Computer Science, BiologyJ. Comput. Chem.
- 1 September 2007
It is shown that, in fact, 3D descriptor models gave more accurate results than TIs but interestingly, TIs give acceptable results in a timely way in spite of their simplicity.
QSAR model for alignment‐free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP‐lattice networks
This study represents the first example of a QSAR model for the computational chemistry inspired search of potential HBC protein biomarkers and could help to predict the involvement of a certain gene and/or protein in HBC.
A topological sub-structural approach for predicting human intestinal absorption of drugs.
Experimental-Computational Study of Carbon Nanotube Effects on Mitochondrial Respiration: In Silico Nano-QSPR Machine Learning Models Based on New Raman Spectra Transform with Markov-Shannon Entropy…
This work is aimed at demonstrating that the SG transform of Raman spectra is useful to encode CNT information, similarly to theSG transform of the blood proteome spectra in cancer or electroencephalograms in epilepsy and also as a prospective chemoinformatics tool for nanorisk assessment.
Unified QSAR and network‐based computational chemistry approach to antimicrobials, part 1: Multispecies activity models for antifungals
This work developed a multispecies QSAR classification model, in which the outputs were the inputs of the aforementioned network, and represented it as a large network, which may be used to identify drugs with similar mechanism of action.
TOPS-MODE Based QSARs Derived from Heterogeneous Series of Compounds. Applications to the Design of New Herbicides
- M. P. González, H. Díaz, Reinaldo Molina Ruiz, Miguel A. Cabrera, Ronal Ramos de Armas
- Mathematics, Computer ScienceJ. Chem. Inf. Comput. Sci.
- 12 June 2003
The present TOPS-MODE based QSAR is the first alternate general "in silico" technique to experimentation in herbicides discovery and shows an overall predictability of 91% and 92% for active and inactive compounds, being the global percentage of good classification of 92%.
Symmetry considerations in Markovian chemicals 'in silico' design (MARCH-INSIDE) I: central chirality codification, classification of ACE inhibitors and prediction of \sigma-receptor antagonist…