Search results for " graph"
showing 10 items of 1277 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 …
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.…
Algorithms on Graphs
1988
In this chapter we shall develop some basic algorithms for directed graphs and relations which will be of use in later chapters, where the efficient construction of parsers is considered. The constructions needed can be expressed as the computing of certain “relational expressions”. These are expressions whose operands are relations and whose operators are chosen from among multiplication, closure, union and inverse. For this purpose we need to develop an algorithm for computing the closure of a relation. In view of the nature of our applications, the most appropriate way to do this is by a depth-first traversal of the graph that corresponds to the given relation. Other ways of computing th…
Bɪ-CомDᴇт: Community Detection in Bipartite Networks
2019
Abstract Extracting hidden communities from bipartite networks witnessed a determined effort. In this respect, different streams of research relied on bipartite networks to unveil communities. In this paper, we introduce a new approach, called Bi-Comdet, that aims to an efficient community detection in bipartite networks. The main trust of the introduced approach is that it stresses on the importance of grouping two types of nodes in communities having a full connection between its nodes. The quality of the unveiled communities, is assessed through some metrics borrowed from the FCA community, to wit modularity, overlapping and stability. These metrics are then aggregated through the use of…
Modélisation de l’évolution d’un finage, du rural au périurbain (Montagne bourguignonne)
2007
La transformation accélérée des rapports entre les sociétés villageoises et leur territoire a des conséquences de nature à la fois organisationnelle, biophysique et agronomique: les opérations d'aménagement rural y trouvent leur justification. Une démarche de diagnostic de territoire a été élaborée et mise en oeuvre à l'occasion de ces opérations. Un itinéraire méthodologique permet de construire un «modèle morpho-historique» qui rend des interrelations entre milieu physique et histoire d'un lieu, à travers un système de relations territorialisé. Le modèle «MH» permet, dans le cadre de procédures d'aménagement, de repérer des portions de territoire «sensibles».