Rapporteur, ensc, Montpellier








télécharger 0.86 Mb.
titreRapporteur, ensc, Montpellier
page18/22
date de publication22.04.2017
taille0.86 Mb.
typeRapport
c.21-bal.com > comptabilité > Rapport
1   ...   14   15   16   17   18   19   20   21   22






Frameworks

Scaffolds

Chaînes latérales

RECAP

Diversité Globale

Diversité Relative

ACB Blocks

830

3589

125

7545

3.7810

6.174E-05

AnalytiCon Discovery

981

3980

188

886

1.4142

1.634E-04

Asinex

17489

78088

4971

47699

43.8819

1.269E-04

Aurora Fine Chemicals

1674

6968

1349

6484

11.2228

3.561E-04

BioFocus

2039

6431

181

1167

2.1998

9.277E-05

CB R&D

10

39

35

97

0.2920

1.659E-03

Cerep

4505

11017

516

2435

5.6380

2.808E-04

ChemBridge

15927

89921

5562

53186

48.6846

1.143E-04

ChemDiv

27118

119920

5779

70460

58.0721

1.050E-04

ChemStar

5497

19677

2244

16309

19.5807

3.261E-04

ChemT&I

12496

59863

3446

35202

31.4484

6.486E-05

Chim. Nat.

2666

10743

2472

11545

17.3702

6.597E-04

Combi-Blocks

30

157

127

288

0.9784

9.274E-04

CombiPure

109

312

35

193

0.1955

2.149E-04

EMC Microcollections

1343

3808

245

2504

2.0814

8.696E-05

Enamine

30930

148325

6032

56913

59.7260

1.395E-04

Florida Center for Heterocyclic Compounds

2651

10786

3043

11021

18.6212

6.309E-04

Frontier Scientific

40

196

86

166

1.0577

1.731E-03

ICOA

603

1630

545

1984

3.8402

1.195E-03

InFarmatik

78

289

73

242

0.7832

1.448E-03

InterBioScreen

19754

86924

6120

56117

50.7324

1.192E-04

KeyOrganics

5711

26980

2336

21606

20.8891

1.117E-04

LaboTest

295

1202

528

1441

5.3080

1.714E-03

Matrix Scientific

437

3118

893

2948

8.1409

5.441E-04

MayBridge

4520

25620

3081

20461

27.6731

4.003E-04

MDPI

1349

4649

1055

4158

10.2281

1.003E-03

MedChemLab

7687

28788

1842

22330

18.8797

1.053E-04

NCI

16428

81368

18382

72993

89.7036

3.670E-04

Otava

5119

18895

1644

13261

15.7044

2.044E-04

Prestwick

340

771

348

1009

2.6623

2.383E-03

Specs

15909

64567

4645

53730

46.6398

2.125E-04

Spectrum Info

217

462

107

535

1.1340

9.618E-04

SynChem

46

243

52

304

0.8165

1.384E-03

SynphaBase

36

84

72

154

0.6202

4.219E-03

TimTec

24173

118531

7906

86653

69.5710

1.057E-04

TOSLab

3317

8487

768

8426

8.5838

3.694E-04

Tripos

4942

20964

1067

5142

8.0493

1.233E-04

VitasM Laboratory

10752

46581

3482

32066

29.9402

1.323E-04

IV. Manuel d’utilisation de ScreeningAssistant

ScreeningAssistant Manual


More scientific details about the software can be found here.

NEEDED SOFTWARES

Before you can use ScreeningAssistant, 3 softwares must be installed on your computer:

  • Java 5 JRE (ScreeningAssistant won't work with previous Java virtual machine)

  • Java3D (Java3D must be installed AFTER Java 5 JRE)

  • A MySQL server to manage databases. It is recommended to run MySQL on a separated Linux computer. However, for testing purpose, you can use EasyPHP. EasyPHP is a Windows software which automatically installs a MySQL server on your computer.

  • Optionally, you can use Marvin as molecular viewer by adding MarvinBeans.jar to your classpath. If you don't have Marvin, ScreeningAssistant will use its internal molecular viewer (JOELib molecular viewer).

FOR USERS OF A PREVIOUS VERSION OF SCREENINGASSISTANT

This new version introduces changes in the structure of the database used by ScreeningAssistant. In consequence you can't use this new version directly with a database created with a previous version of ScreeningAssistant. Your old databases need to be updated. It could be done using a little java program. Here is an example for updating a database named MyDataBase:




In this example the MySQL server is installed on this computer, the user name is Toto and his password is MyPassword.

USER GUIDE

The ScreeningAssistant desktop environment: create your first database

Launch your MySQL server (e.g. easyPHP) and double-click on the ScreeningAssistant icon on your desktop.

(You must launch EasyPHP each time you want to use ScreeningAssistant. EasyPHP launch two softwares: Apache (a web server) and MySQL. Apache don't need to be started, only MySQL wil be used by ScreeningAssistant.)

The following windows will appear on the screen :




You can see that only an internal window is open, the molecule viewer, which is empty. ScreeningAssistant GUI is built as a virtual desktop, and it means that you can minimize, resize and move the opened windows. First thing to do is to open an existing database or to create a new one. To do this open the Database menu and click on New.




In the login window, enter the server's IP address (127.0.0.1 if you use EasyPHP on your computer), a user name of a MySQL administrator account and the corresponding password (by default MySQL admin name is "root" with no password).




Clicking OK in the login window will let you create a new database or open an existing one. To create a new database, enter the name in the text box and click create. To open an existing database select it and click Open. You can also delete a selected database.




When a database is opened, you can see its compounds in the Database Viewer window. Grey rows means that corresponding molecules are estimated as not drug-like. Clicking in any row of the database viewer will display the molecule in the structure viewer.




At your first use you won't have any row in your Database Viewer. The next step will be to import a SDF.

The menu bar: import/export compounds and analyse your database




To append compounds in the database go to the Database menu of the Database Viewer window, and click Append.



In the Append window, firstly you must choose the file to import. If "Add all SDF of this directory" is set to Yes, you must be sure that all the SDF of the directory have the same ID and CAS field names.
Then, you must choose which field names corresponds to ID field and CAS field. CAS field is optional, but you must define ID field. In the provider part, you can choose the provider of the compounds, either an existing one or a new one (you must then define at least the Name field). Click OK to begin the importation process.




To export the selection of the Database Viewer (we will explain how to change the selection in the tool bar part of this manual), click on Export in the Database menu. In the export window, you can define name of the exported file and its type. If you have minimized structures with Corina, you can choose to export only correctly minimized structures.

If a number is entered in the field "Diversity: number of compounds to select", then a diversity algorithm will be used to select a number of compounds close to the number entered (the number of compounds exported by diversity can't be specified exactly). Diversity algorithm is quick for a small number of compounds, but can be very long for million structures !


Many charts are available in ScreeningAssistant :

  • Pie Charts : compounds by providers

    • Compounds Repartition

    • Drug-like

    • Lead-like

  • Percentages

    • Drug-like

    • Lead-like

  • Distribution

    • Molecular Weight

    • Number of H bond acceptors

    • Number of H bond donors

    • LogP

    • Number of rotatable bonds

    • TPSA

  • Internal Duplicates

  • Unicity: compound not present in the databases of the other providers

  • Frameworks: number of different frameworks by providers

  • Diversity: estimated with the number of clusters created by the SCA algorithm with 0.8 cut-off

    • Global

    • Drug-like

    • Lead-like

  • Chemical Space: display selected compounds in a chemical space. The axis are defined by the PCA1 and PCA2 axis equations obtained from the PCA analysis of 18 000 compounds selected by diversity among 2.6 millions.

At the present time, only the minimization of the compounds by Corina is available. Of course you need the corina.exe file in your computer to use this option. Once corina.exe put in the ScreeningAssistant\external\corina directory, you can minimize compounds of your databases.



1   ...   14   15   16   17   18   19   20   21   22

similaire:

Rapporteur, ensc, Montpellier iconDe la franc maconnerie a montpellier
Écrit à son ami Pierre Jacques Astruc, conseiller maître en la cour des comptes, aides et finances de Montpellier

Rapporteur, ensc, Montpellier iconEconomies d’eau : Réutilisation des eaux de pluie
«Eaux» de l’Afssa 15 cnrs- umr 5119-Université Montpellier 2- montpellier 16 ehesp- rennes 17 Laboratoire de Santé publique et Environnement-Faculté...

Rapporteur, ensc, Montpellier iconÉconomies d’eau : Réutilisation des eaux de pluie
«Eaux» de l’Afssa 15 cnrs- umr 5119-Université Montpellier 2- montpellier 16 ehesp- rennes 17 Laboratoire de Santé publique et Environnement-Faculté...

Rapporteur, ensc, Montpellier iconRapporteur

Rapporteur, ensc, Montpellier iconRapporteur : Saddek Aouadi, Professeur, Université d’Annaba

Rapporteur, ensc, Montpellier iconRapporteur trigonométrique circulaire pour série générale et technologique...

Rapporteur, ensc, Montpellier iconCmi montpellier informatique

Rapporteur, ensc, Montpellier iconSociete regionale de medecine et d’hygiene du travail de montpellier

Rapporteur, ensc, Montpellier iconRapporteur : Philippe Cléris Le Grand Paris et l’Eure. Ou un début...

Rapporteur, ensc, Montpellier iconL ycee agricole prive
«blanco», équerre, compas, rapporteur, taille-crayon, crayon à papier, double décimètre, stylos noir, bleu, vert, rouge et crayons...








Tous droits réservés. Copyright © 2016
contacts
c.21-bal.com