Rapporteur, ensc, Montpellier

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titreRapporteur, ensc, Montpellier
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The tool bar: navigate in your database and select compounds

The database viewer displays 1000 molecules by page. You can change the pages using the five blue icons. The   icon allows to directly go to a page entering is number.

You can select desired compounds using the  icon.

You can select the providers. By default all providers are selected. In the query part of the screen you can define filters for the selection. You must choose the parameter, the equality sign, the value and then click Add to define a new parameter. There is no limit in the number of filters you can define.


  • id: internal ID of the compound

  • md5ichi: hascode of the unique identifier

  • mw: molecular weight of the compounds, without counter-ion(s) and at pH=7

  • logP

  • TPSA: Topological Polar Surface Area

  • Hba: number of H bond acceptors

  • Hbd: number of H bond donors

  • rotatable bonds

  • halogens

  • single_chains: single chains longer than ≤ -(CH2)6CH3 (0 for no, 1 for yes)

  • perfluorinated_chain: presence of -CF2CF2CF3 (0 for no, 1 for yes)

  • SSSRs: number of Smallest Sets of Smallest Rings

  • big_ring_size: size of the bigger ring found by SSSRs

  • O: number of O atoms

  • N: number of N atoms

  • S: number of S atoms

  • NO2: number of NO2

  • SO2: number of SO2

  • CF3: number of CF3

  • CF3_halogens: number of CF3 and other halogen atoms

  • NOS: number of N, O and S atoms

  • bad_atoms: number of atoms other than C, O, N, S, P, F, Cl, Br, I, Na, K, Mg, Ca, or Li

  • is_reactive: presence of a reactive function (0 for no, 1 for yes)

  • is_warhead: presence of a warhead type substructure (0 for no, 1 for yes)

  • is_promiscuous: the molecule is known to be a promiscuous inhibitor (0 for no, 1 for yes)

  • is_privileged: if > -1, then a privileged structure is detected in the structure of the molecule

  • absorption: not used yet

  • caco2: not used yet

  • solubility: not used yet

  • BBB: not used yet

  • drug-like_failures: number of non-fitted drug-like criteria

  • lead-like_failures: number of non-fitted lead-like criteria

  • PDL_score: our internal Progressive 'Drug-Like' score. ≤ 1 means the compounds is estimated drug-like, more than 2 means the compounds is absolutely not drug-like

  • PLL_score: our internal Progressive 'Lead-Like' score. ≤ 1 means the compounds is estimated lead-like, more than 2 means the compounds is absolutely not lead-like

  • CFMS: Cleaning For My Screening. By default it is based on PDL and add penalties for the presence of reactive functions, warheads, primiscuous aggregating inhibitors, single chains, perfluorinated chains, and for the abscence of N or O

  • scaffold: scaffold id (scaffold used is rings + linkers)

  • framework: id of the general 2D shape of the molecule

  • ClogP: not used yet.

  • entrie_date

Example of a drug-like selection:

Example of a selection for screening:

A screening selection can be done in the same way that a drug-like selection, but using the criteria bad_atoms=0 and CFMS=0. By default, CFMS is the same thing that PDL, but it takes into account additional features such as reactive functions.

CFMS can be personalized using the   icon. Then, you can choose the base of CFMS ('drug-like' or 'lead-like' i.e. PDL or PLL) the additional penalties can be chosen. Clicking Ok after user's choices will recompute the new CFMS value for all the compounds of the current database.

The reactive functions and warheads penalties can also be personalized through Configure in the main menu of ScreeningAssistant :

The False Positive Filters window is now open:

This window will allow you to modify definitions of reactive functions and warheads. You can create and delete sub-structures filters using New and Delete buttons. The name of a property can be changed double clicking on it. The Structure field let you to edit the SMARTS code of the filter. If you have MarvinBeans.jar in your classpath, the sub-structure can be edited graphically.

The modification of the filters will apply when new compounds are added.

2D chemical space covered by the selected compounds can be viewed using the  icon. Here is an example of chemical space:

This chemical space use the PCA1 and PCA2 axis equation computed on 18 000 diverse molecule selected from 2.6 millions with the descriptors used are SSKey3DS, MW and logP.

i Nous utiliserons dans le suite de ce document le terme « liaisons pouvant tourner » comme traduction du terme anglo-saxon « rotatable bonds ». Les terminologies françaises et anglaises sont réductrices de la notion. Une définition détaillée de ce type de liaison est donné chapitre 2 partie II. B. 8. a.

i Un code de hachage est le résultat de la conversion par une fonction de hachage d’un grand ensemble en un ensemble plus petit. La fonction MD5 permet ainsi de convertir un ensemble de données de n’importe quelle taille en une chaîne de 32 caractères hexadécimaux (128 bits).

ii Nous avons gardé le terme anglosaxon fingerprint, car la traduction française « empreinte digitale » n’est généralement pas employé en chemoinformatique. Nous utiliserons ce mot au masculin.

i La notation de « O », appelée notation de Landeau, est utilisée pour indiquer à quelle vitesse une fonction augmente ou diminue. Cette notation est très utilisée pour définir la complexité d’un algorithme. Des explications détaillées sont disponibles à l’adresse suivante : http://fr.wikipedia.org/wiki/Notations_de_Landau

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