Search results for "graphics"
showing 10 items of 1223 documents
Molecular volumes and surfaces of biomacromolecules via GEPOL: A fast and efficient algorithm
1990
A triangular tesselation approach to build up surfaces has been adapted to the study of biomolecules. By using a data-coded generic pentakisdodecahedron each atom is assigned a particular sphere whose radii are chosen according to any suitable property. Different types of surfaces have been adapted to this method: van der Waals, surface accessible, and Richard's molecular surface. A simple method is used to eliminate all triangles found at the intersection volume of the atomic spheres and a fast algorithm is employed to calculate the area of the envelope surface and the volume therein. The data about the surface are given by the coordinates of the center of each triangle, elementary surface…
Exploiting a list of protein sequences
2007
Abstract: We describe a software program to help exploit a database of aligned protein sequences. In addition to the classical lists of sequences, a graphical representation is used to get a better overview of the information. As natural parameters, the type of amino acid and sequence position are used. Various plots or 3D representations are then updated. Examples are shown based on globin sequences from various species and on the abnormal human hemoglobins. The software should be of interest to protein engineers who need to know what variants are already known.
General topological patterns of known drugs.
2001
Abstract Discriminating “drug-like” from “non-drug-like” compounds is a relatively emerging topic within the drug research. The basic assumption is that it is possible to obtain relevant information from structural features common to the known drugs, in order to discard a huge number of candidate chemical structures with low probability of becoming drugs. A graph-theoretical contribution to this subject is reported in this paper, by making exclusive use of linear relationships. The results suggest that it is possible to achieve a pattern of general pharmacological activity based on molecular topology. Conclusions are tentative pending verification of the results with larger compound librari…
A DFT study of [3 + 2] cycloaddition reactions of an azomethine imine with N-vinyl pyrrole and N-vinyl tetrahydroindole
2016
The mechanism and selectivities of the [3+2] cycloaddition (32CA) reactions of azomethine imine (AI) 8 with two N-vinyl five-membered heterocycles (NVFH), 9a and 9b, have been theoretically studied using DFT methods at the MPWB1K/6-31G(d) computational level. The possible ortho/meta regio- and endo/exo stereoselective channels were explored and characterised. The low polar character of these 32CA reactions, which is the consequence of the high nucleophilic character of both reagents, as well as the non-effective reactivity of these NVFH as nucleophiles, accounts for the high calculated activation energies, 16.1 (9a) and 16.8 (9b) kcalmol-1 in chlorobenzene. Analysis of the relative electron…
Divulging the various chemical reactivity of trifluoromethyl-4-vinyl-benzene as well as methyl-4-vinyl-benzene in [3+2] cycloaddition reactions.
2020
Abstract In the present paper, an investigation about the [3 + 2]cycloaddition (32 C A) reactions of benzonitrile oxide with 1-trifluoromethyl-4-vinyl-benzene, and with 1-methyl-4-vinyl-benzene, using the Molecular Electron Density Theory (MEDT) through DFT/B3LYP/6–311++G (d,p), is performed. A deep mechanistic study beside an accurate electronic description of different stationary points along the IRC paths of the two 32 C A reactions have performed by examining the two competitive regioisomericortho/metareaction pathways, and providing the mechanism associated with them. The presence of the CF3 group reduces the activation energy, which makes it possible to increase the experimental yield…
Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site.
2010
The protein structure-based virtual screening is typically accomplished using a molecular docking procedure. However, docking is a fairly slow process that is limited by the available scoring functions that cannot reliably distinguish between active and inactive ligands. In contrast, the ligand-based screening methods that are based on shape similarity identify the active ligands with high accuracy. Here, we show that the usage of negative images of the ligand-binding site, together with shape comparison tools, which are typically used in ligand-based virtual screening, improve the discrimination of active molecules from inactives. In contrast to ligand-based shape comparison, the negative …
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
Enhancing dynamic graphical analysis with the Lisp-Stat language and the ViSta statistical program
2005
Presented is a sample of computerized methods aimed at multidimensional scaling and psychometric item analysis that offer a dynamic graphical interface to execute analyses and help visualize the results. These methods show how the Lisp-Stat programming language and the ViSta statistical program can be jointly applied to develop powerful computer applications that enhance dynamic graphical analysis methods. The feasibility of this combined strategy relies on two main features: (1) The programming architecture of ViSta enables users to add new statistical methods as plug-ins, which are integrated into the program environment and can make use of all the functions already available in ViSta (e.…
Méthodes de contrôle de la rugosité à partir des propriétés différentiels de courbes autosimilaires.
2023
La rugosité a de nombreuses applications, l’industrie l’utilise comme outil pour avoir des propriétés de surface recherchés ou pour le contrôle qualité, le domaine de l’informatique graphique s’intéresse à la synthétiser pour la génération de terrains ou la génération de textures et aussi à simuler ses effets sur la lumière avec les BRDF. . . Dans cette présentation, nous proposeronsun rappel sur la rugosité, notamment sa définition plus précise que "surface ou courbe non lisse" et ses outils de quantification suivi d’une comparaison de certaines de ses méthodes de génération, illustrant l’intérêt d’une approche fractale pour l’étudier. Nous commencerons par des méthodes simples mais offran…
Fracture Resistance of New Metal-Free Materials Used for CAD-CAM Fabrication of Partial Posterior Restorations
2020
Background and Objectives: To evaluate in vitro the fracture resistance and fracture type of computer-aided design and computer-aided manufacturing (CAD-CAM) materials. Materials and Methods: Discs were fabricated (10 ×