Search results for "Biological system"
showing 10 items of 319 documents
TOMOCOMD-CARDD descriptors-based virtual screening of tyrosinase inhibitors: evaluation of different classification model combinations using bond-bas…
2006
Abstract A new set of bond-level molecular descriptors (bond-based linear indices) are used here in QSAR (quantitative structure–activity relationship) studies of tyrosinase inhibitors, for finding functions that discriminate between the tyrosinase inhibitor compounds and inactive ones. A database of 246 compounds was collected for this study; all organic chemicals were reported as tyrosinase inhibitors; they had great structural diversity. This dataset can be considered as a helpful tool, not only for theoretical chemists but also for other researchers in this area. The set used as inactive has 412 drugs with other clinical uses. Twelve LDA-based QSAR models were obtained, the first six us…
Non-stochastic quadratic fingerprints and LDA-based QSAR models in hit and lead generation through virtual screening: theoretical and experimental as…
2005
In order to explore the ability of non-stochastic quadratic indices to encode chemical information in antimalarials, four quantitative models for the discrimination of compounds having this property were generated and statistically compared. Accuracies of 90.2% and 83.3% for the training and test sets, respectively, were observed for the best of all the models, which included non-stochastic quadratic fingerprints weighted with Pauling electronegativities. With a comparative purpose and as a second validation experiment, an exercise of virtual screening of 65 already-reported antimalarials was carried out. Finally, 17 new compounds were classified as either active/inactive ones and experimen…
String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins.
2011
The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, …
A supramolecular system that strictly follows the binding mechanism of conformational selection
2020
Induced fit and conformational selection are two dominant binding mechanisms in biology. Although induced fit has been widely accepted by supramolecular chemists, conformational selection is rarely studied with synthetic systems. In the present research, we report a macrocyclic host whose binding mechanism is unambiguously assigned to conformational selection. The kinetic and thermodynamic aspects of this system are studied in great detail. It reveals that the kinetic equation commonly used for conformational selection is strictly followed here. In addition, two mathematical models are developed to determine the association constants of the same guest to the two host conformations. A “confo…
Suitability ofMMGBSAfor the selection of correct ligand binding modes from docking results
2018
The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics-generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescor…
Search compounds with antimicrobial activity by applying molecular topology to selected quinolones.
2003
Molecular topology was used to obtain substances with antimicrobial activity. Selected quinolones were employed to develop the corresponding connectivity functions and discriminant equation. Limiting functions were selected that allowed the discriminant function to more efficiently distinguish substances with and without antibacterial activity. Antibacterial tests were run to confirm the theoretically established activity.
Correlation of Pharmacological Properties of a Group of Hypolipaemic Drugs by Molecular Topology
1996
Abstract This investigation was undertaken to test the ability of the molecular connectivity model to predict the percentage of plasma protein binding, the percentage of total cholesterol reduction and oral LD50 in rats of a group of hypolipaemic drugs using multi-variable regression equations with multiple correlation coefficients, standard error of estimate, degrees of freedom, F-Snedecor function values, Mallow's CP and Student's t-test as criteria of fit. Regression analyses showed that the molecular connectivity model predicts these properties. Corresponding stability (cross validation) studies were made on the selected prediction models which confirmed their goodness of fit. The resul…
Development of Methods for the Classification of EVOOs According to Their Geographical Origin
2012
The aim of this work was to obtain the phenolic profiles of EVOOs by using a CEC method, and to evaluate the use of these profiles in the prediction of the geographical origin of these EVOO samples. For this purpose, monolithic columns containing LA and BDDA monomers were constructed.
Microorganisms in the Space Environment
1984
Preliminary results of the Spacelab 1 experiment on the response of Bacillus subtilis spores to conditions of free space are presented. Exposure to the vacuum of space on the Spacelab pallet reduced viability counts about 50 percent and increased mutation frequencies by a factor of about 10. Interpretation of apparent differences in the photobiological and photochemical data between flight and ground simulation experiments will require more statistical analyses and data from actual fluence measurements.
Information decomposition in the frequency domain: a new framework to study cardiovascular and cardiorespiratory oscillations
2021
While cross-spectral and information-theoretic approaches are widely used for the multivariate analysis of physiological time series, their combined utilization is far less developed in the literature. This study introduces a framework for the spectral decomposition of multivariate information measures, which provides frequency-specific quantifications of the information shared between a target and two source time series and of its expansion into amounts related to how the sources contribute to the target dynamics with unique, redundant and synergistic information. The framework is illustrated in simulations of linearly interacting stochastic processes, showing how it allows us to retrieve …