34 research outputs found
Frog: a FRee Online druG 3D conformation generator
In silico screening methods based on the 3D structures of the ligands or of the proteins have become an essential tool to facilitate the drug discovery process. To achieve such process, the 3D structures of the small chemical compounds have to be generated. In addition, for ligand-based screening computations or hierarchical structure-based screening projects involving a rigid-body docking step, it is necessary to generate multi-conformer 3D models for each input ligand to increase the efficiency of the search. However, most academic or commercial compound collections are delivered in 1D SMILES (simplified molecular input line entry system) format or in 2D SDF (structure data file), highlighting the need for free 1D/2D to 3D structure generators. Frog is an on-line service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions. Given the atomic constitution of the molecules and connectivity information, Frog can identify the different unambiguous isomers corresponding to each compound, and generate single or multiple low-to-medium energy 3D conformations, using an assembly process that does not presently consider ring flexibility. Tests show that Frog is able to generate bioactive conformations close to those observed in crystallographic complexes. Frog can be accessed at http://bioserv.rpbs.jussieu.fr/Frog.html
Mutations in SPG11, encoding spatacsin, are a major cause of spastic paraplegia with thin corpus callosum.
Autosomal recessive hereditary spastic paraplegia (ARHSP) with thin corpus
callosum (TCC) is a common and clinically distinct form of familial spastic
paraplegia that is linked to the SPG11 locus on chromosome 15 in most affected
families. We analyzed 12 ARHSP-TCC families, refined the SPG11 candidate interval
and identified ten mutations in a previously unidentified gene expressed
ubiquitously in the nervous system but most prominently in the cerebellum,
cerebral cortex, hippocampus and pineal gland. The mutations were either nonsense
or insertions and deletions leading to a frameshift, suggesting a
loss-of-function mechanism. The identification of the function of the gene will
provide insight into the mechanisms leading to the degeneration of the
corticospinal tract and other brain structures in this frequent form of ARHSP
RPBS: a web resource for structural bioinformatics
RPBS (Ressource Parisienne en Bioinformatique Structurale) is a resource dedicated primarily to structural bioinformatics. It is the result of a joint effort by several teams to set up an interface that offers original and powerful methods in the field. As an illustration, we focus here on three such methods uniquely available at RPBS: AUTOMAT for sequence databank scanning, YAKUSA for structure databank scanning and WLOOP for homology loop modelling. The RPBS server can be accessed at and the specific services at
Lithium intercalated graphite : experimental Compton profile for stage one
Electron momentum distribution of the first stage lithium intercalated graphite (LiC6) is measured by X-ray inelastic scattering and compared to the graphite one, using the high resolution spectrometer from LURE-DCI synchrotron source. The Compton profile difference is consistent with a total transfer of the lithium conduction electron to a Ï band as expected in a rigid band model. But this model is clearly insufficient to explain all the measured profile difference features which reflect the total electronic change in intercalation.La distribution d'impulsions Ă©lectroniques du composĂ© intercalaire du graphite de premier stade LiC6 est mesurĂ©e par diffusion inĂ©lastique de photons X et comparĂ©e Ă celle du graphite, grĂące au spectromĂštre Ă haute rĂ©solution de LURE-DCI. La diffĂ©rence des profils Compton est compatible avec un transfert total de l'Ă©lectron de conduction du lithium vers une bande Ï comme le prĂ©voit un modĂšle de bandes rigides. Mais ce modĂšle est insuffisant pour expliquer tous les aspects du profil diffĂ©rence qui sont en fait l'illustration de la modification Ă©lectronique due Ă l'insertion
HYBRIDIZATION EFFECTS IN SOLIDS STUDIED BY COMPTON SCATTERING
Nous présentons une série de mesures de profils Compton
sur des cristaux de LiH et de LiC6. La comparaison avec les profils
calculĂ©s permet de tester la qualitĂ© des fonctions d'onde du systĂšme, et par lĂ
de vérifier si la base de fonctions d'onde utilisées pour créer les orbitales
prend en compte toutes les hybridations Ă©ventuelles.We present a serie of measurements of Compton profiles on
LiH and LiC6 crystals.The comparison with calculated profiles is a
test of the quality of the wave function of the system, and it allows to check
if the basis set used to develop the wave function takes care of all eventual
hybridizations