Search results for "Models"
showing 10 items of 8211 documents
Extended GT-STAF information indices based on Markov approximation models
2013
Abstract A series of novel information theory-based molecular parameters derived from the insight of a molecular structure as a chemical communication system were recently presented and usefully employed in QSAR/QSPRs (J. Comp. Chem, 2013, 34, 259; SAR and QSAR in Environ. Res. 2013, 24). This approach permitted the application of Shannon’s source and channel coding entropic measures to a chemical information source comprised of molecular ‘fragments’, using the zero-order Markov approximation model (atom-based approach). This report covers the theoretical aspects of the extensions of this approach to higher-order models, introducing the first, second and generalized-order Markov approximati…
A topological substructural approach for the prediction of P-glycoprotein substrates
2006
A topological substructural molecular design approach (TOPS-MODE) has been used to predict whether a given compound is a P-glycoprotein (P-gp) substrate or not. A linear discriminant model was developed to classify a data set of 163 compounds as substrates or nonsubstrates (91 substrates and 72 nonsubstrates). The final model fit the data with sensitivity of 82.42% and specificity of 79.17%, for a final accuracy of 80.98%. The model was validated through the use of an external validation set (40 compounds, 22 substrates and 18 nonsubstrates) with a 77.50% of prediction accuracy; fivefold full cross-validation (removing 40 compounds in each cycle, 80.50% of good prediction) and the predictio…
New tyrosinase inhibitors selected by atomic linear indices-based classification models.
2005
In the present report, the use of the atom-based linear indices for finding functions that discriminate between the tyrosinase inhibitor compounds and inactive ones is presented. In this sense, discriminant models were applied and globally good classifications of 93.51% and 92.46% were observed for non-stochastic and stochastic linear indices best models, respectively, in the training set. The external prediction sets had accuracies of 91.67% and 89.44%. In addition, these fitted models were used in the screening of new cycloartane compounds isolated from herbal plants. A good behavior is shown between the theoretical and experimental results. These results provide a tool that can be used i…
Modeling the chiral resolution ability of highly sulfated β-cyclodextrin for basic compounds in electrokinetic chromatography
2013
Abstract Despite the fact that extensive research in the field of enantioseparations by capillary electrophoresis has been carried out, it is difficult to predict whether a concrete chiral selector would be useful for the separation of a racemic compound. Hence, several experimental effort is necessary to test the abilities of individual chiral selectors, usually by trial and error procedures. Thus, the enantioseparation of a new racemate becomes a time- and money-consuming task. In this work, the ability of highly sulfated β-cyclodextrin (HS-β-CD) as chiral selector in electrokinetic chromatography (EKC) is modeled for the first time, using exclusively directly-available structural data of…
New active drugs against liver stages of Plasmodium predicted by molecular topology.
2008
ABSTRACT We conducted a quantitative structure-activity relationship (QSAR) study based on a database of 127 compounds previously tested against the liver stage of Plasmodium yoelii in order to develop a model capable of predicting the in vitro antimalarial activities of new compounds. Topological indices were used as structural descriptors, and their relation to antimalarial activity was determined by using linear discriminant analysis. A topological model consisting of two discriminant functions was created. The first function discriminated between active and inactive compounds, and the second identified the most active among the active compounds. The model was then applied sequentially t…
Vanilloid Derivatives as Tyrosinase Inhibitors Driven by Virtual Screening-Based QSAR Models
2010
A number of vanilloids have been tested as tyrosinase inhibitors using Ligand-Based Virtual Screening (LBVS) driven by QSAR (Quantitative Structure-Activity Relationship) models as the multi-agent classification system. A total of 81 models were used to screen this family. Then, a preliminary cluster analysis of the selected chemicals was carried out based on their bioactivity to detect possible similar substructural features among these compounds and the active database used in the QSAR model construction. The compounds identified were tested in vitro to corroborate the results obtained in silico. Among them, two chemicals, isovanillin (K(M) (app) = 1.08 mM) near to kojic acid (reference d…
Atom, atom-type, and total nonstochastic and stochastic quadratic fingerprints: a promising approach for modeling of antibacterial activity.
2005
The TOpological MOlecular COMputer Design (TOMOCOMD-CARDD) approach has been introduced for the classification and design of antimicrobial agents using computer-aided molecular design. For this propose, atom, atom-type, and total quadratic indices have been generalized to codify chemical structure information. In this sense, stochastic quadratic indices have been introduced for the description of the molecular structure. These stochastic fingerprints are based on a simple model for the intramolecular movement of all valence-bond electrons. In this work, a complete data set containing 1006 antimicrobial agents is collected and presented. Two structure-based antibacterial activity classificat…
Modeling Natural Anti-Inflammatory Compounds by Molecular Topology
2011
One of the main pharmacological problems today in the treatment of chronic inflammation diseases consists of the fact that anti-inflammatory drugs usually exhibit side effects. The natural products offer a great hope in the identification of bioactive lead compounds and their development into drugs for treating inflammatory diseases. Computer-aided drug design has proved to be a very useful tool for discovering new drugs and, specifically, Molecular Topology has become a good technique for such a goal. A topological-mathematical model, obtained by linear discriminant analysis, has been developed for the search of new anti-inflammatory natural compounds. An external validation obtained with …
Witnessing objectivity on a quantum computer
2021
Understanding the emergence of objectivity from the quantum realm has been a long standing issue strongly related to the quantum to classical crossover. Quantum Darwinism provides an answer, interpreting objectivity as consensus between independent observers. Quantum computers provide an interesting platform for such experimental investigation of quantum Darwinism, fulfilling their initial intended purpose as quantum simulators. Here we assess to what degree current NISQ devices can be used as experimental platforms in the field of quantum Darwinism. We do this by simulating an exactly solvable stochastic collision model, taking advantage of the analytical solution to benchmark the experime…
Spin‐Chain‐Star Systems: Entangling Multiple Chains of Spin Qubits
2022
We consider spin-chain-star systems characterized by N-wise many-body interactions between the spins in each chain and the central one. We show that such systems can be exactly mapped into standard spin-star systems through unitary transformations. Such an approach allows the solution of the dynamic problem of an XX$X X$ spin-chain-star model and transparently shows the emergence of quantum correlations in the system, based on the idea of entanglement between chains.