Search results for "Computation"
showing 10 items of 7362 documents
Analytical chemistry on many-center chiral compounds based on vibrational circular dichroism: Absolute configuration assignments and determination of…
2019
The absolute configuration of a chiral molecule is key to its biological activity. Being able to find out what this configuration is, is thus crucial for a wide range of applications. The difficulties associated with such a determination steeply rise as the number of chiral centers in a given compound becomes larger. Concurrently, it becomes increasingly more challenging to determine the levels and identity of potential stereochemical contaminants in a given sample with one and the same technique, leading in practice to extensive and laborious efforts employing multiple analytical techniques. Here, experimental and theoretical studies based on Vibrational Circular Dichroism (VCD) are presen…
The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part I: gas phase.
2014
The vibronic spectra of the green fluorescent protein chromophore analogues p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) and 3,5-tert-butyl-HBDI (35Bu) are similar in the vacuum, but very different in water or ethanol. To understand this difference, we have computed the vibrationally resolved solution spectra of these chromophores, using the polarizable continuum model (PCM) to account for solvent effects on the (harmonic) potential energy surfaces (PES). In agreement with experiment, we found that the vibrational progression increases with the polarity of the solvent, but we could neither reproduce the broadening, nor the large difference between the absorption spectra of HBDI and…
Hierarchical Parallelization of an H.264/AVC Video Encoder
2006
Last generation video encoding standards increase computing demands in order to reach the limits on compression efficiency. This is particularly the case of H.264/AVC specification that is gaining interest in industry. We are interested in applying parallel processing to H.264 encoders in order to fulfill the computation requirements imposed by stressing applications like video on demand, videoconference, live broadcast, etc. Given a delivered video quality and bit rate, the main complexity parameters are image resolution, frame rate and latency. These parameters can still be pushed forward in such a way that special purpose hardware solutions are not available. Parallel processing based on…
Comparative theoretical study of transition structures, barrier heights, and reaction energies for the intramolecular tautomerization in acetaldehyde…
1998
The transition structures associated with the possible intramolecular tautomerization for acetaldehyde/vinyl alcohol and acetaldimine/vinylamine systems as models of keto/enol and imine/enamine interconversion processes, respectively, were characterized. The relative stabilities of the tautomers and the associated barrier heights were calculated. Ab initio analytical gradients and second derivatives at the HF level of theory and 3-21G, 6-31G, 6-31G**, 6-31++G**, and 6-311++G** basis-set, DFT (BP86/6-311++G** and BLYP/6-311++G**), and semiempirical (AM1 and PM3) procedures were used to identify the stationary points. Correlation effects were estimated using the perturbational approach at MP2…
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
2015
Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the de…
An Embedded Real-Time Lane-Keeper for Automatic Vehicle Driving
2008
Automatic vehicle driving involves several issues, such as the capability to follow the road and keep the right lane, to maintain the distance between vehicles, to regulate vehiclepsilas speed, to find the shortest route to a destination. In this paper a real-time automatic lane-keeper is proposed. The main features of the system are the lane markers location process as well as the computation of the vehiclepsilas steering lock. The above techniques require high elaboration speed to execute, check and complete an operation before a prearranged time. Clearly if system processing exceeds the deadline, the whole operation became meaningless or, in the meantime, the vehicle can reach a critical…
A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Rec…
2016
Molecular dynamics (MD) simulations can be used, prior to virtual screening, to add flexibility to proteins and study them in a dynamic way. Furthermore, the use of multiple crystal structures of the same protein containing different co-crystallized ligands can help elucidate the role of the ligand on a protein's active conformation, and then explore the most common interactions between small molecules and the receptor. In this work, we evaluated the contribution of the combined use of MD on crystal structures containing the same protein but different ligands to examine the crucial ligand-protein interactions within the complexes. The study was carried out on peroxisome proliferator-activat…
An approach to identify new antihypertensive agents using Thermolysin as model: In silico study based on QSARINS and docking
2019
Thermolysin is a bacterial proteolytic enzyme, considered by many authors as a pharmacological and biological model of other mammalian enzymes, with similar structural characteristics, such as angiotensin converting enzyme and neutral endopeptidase. Inhibitors of these enzymes are considered therapeutic targets for common diseases, such as hypertension and heart failure. In this report, a mathematical model of Multiple Linear Regression, for ordinary least squares, and genetic algorithm, for selection of variables, are developed and implemented in QSARINS software, with appropriate parameters for its fitting. The model is extensively validated according to OECD standards, so that its robust…
Applying pattern recognition methods plus quantum and physico-chemical molecular descriptors to analyze the anabolic activity of structurally diverse…
2008
The great cost associated with the development of new anabolic-androgenic steroid (AASs) makes necessary the development of computational methods that shorten the drug discovery pipeline. Toward this end, quantum, and physicochemical molecular descriptors, plus linear discriminant analysis (LDA) were used to analyze the anabolic/androgenic activity of structurally diverse steroids and to discover novel AASs, as well as also to give a structural interpretation of their anabolic-androgenic ratio (AAR). The obtained models are able to correctly classify 91.67% (86.27%) of the AASs in the training (test) sets, respectively. The results of predictions on the 10% full-out cross-validation test al…
In Silico Prediction of Caco-2 Cell Permeability by a Classification QSAR Approach
2011
In the present study, 21 validated QSAR models that discriminate compounds with high Caco-2 permeability (Papp ≥8×10(-6) cm/s) from those with moderate-poor permeability (Papp <8×10(-6) cm/s) were developed on a novel large dataset of 674 compounds. 20 DRAGON descriptor families were used. The global accuracies of obtained models were ranking between 78-82 %. A general model combining all types of molecular descriptors was developed and it classified correctly 81.56 % and 83.94 % for training and test sets, respectively. An external set of 10 compounds was predicted and 80 % was correctly assessed by in vitro Caco-2 assays. The potential use of the final model was evaluated by a virtual s…