Difference between revisions of "Development of a method for the generation of GPCR-ligands libraries"

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(New page: {{Projectproposal |Contact person=Jaap Heringa |Master areas=Bioinformatics |Fulfilled=No }} ==PROFILE OF THE DEPARTMENT OF MOLECULAR DESIGN & INFORMATICS FOR AN INTERNSHIP OR GRADUATION==...)
 
 
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{{Projectproposal
 
|Contact person=Jaap Heringa
 
|Contact person=Jaap Heringa
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|Contact person2=Jan Klomp (Schering-Plough)
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|Contact person3=Monique Hermers (Schering-Plough)
 
|Master areas=Bioinformatics
 
|Master areas=Bioinformatics
 
|Fulfilled=No
 
|Fulfilled=No

Latest revision as of 16:16, 7 February 2014


About Development of a method for the generation of GPCR-ligands libraries


Description

PROFILE OF THE DEPARTMENT OF MOLECULAR DESIGN & INFORMATICS FOR AN INTERNSHIP OR GRADUATION

Education level: WO Period: 6-12 months

Study: Bioinformatic, Chemoinformatica, Molecular Modeling

Department: MDI

Internship coordinator: Monique Hermers

Contact: Jan Klomp

Introduction:

The MDI department is, involved in in-silico drug development/evaluation and 3D structure analysis. Using a.o. Bioinformatics, Chemoinformatics. General description activities: Development of a method for the generation of GPCR-ligands libraries. Possibilitie(s) / Subject(s) for internship: One of the main target families in drug discovery is the superfamily of G-protein coupled receptors (GPCRs). The human genome contains roughly 800 different members of this family, which can be divided in groups based on amino acid sequence similarity. The assumption that small molecules (similar to 11-cis retinal in bovine rhodopsin) bind to the upper part of the 7 transmembrane helices allows a general selection of residues (or residue positions) which might interact with ligands.

Goal:

In silico analyses of G-protein coupled receptors (GPCRs) and small molecule ligands.

  1. Analysis on the amino acid sequences in general and more specific the amino acids

contributing to the assumed binding pockets.

  1. Analysis of the GPCR ligands present in drugs databases (e.g.WDI).
  2. Deduce multiple binding hypotheses (pharmacophores, key features and or property

profiles), which will be used in virtual screening and library design.

Information and contact:

For more information, please contact Jan Klomp [1], telephone: 0412 - 661383. For more information about internship procedures please contact the department of Internship coordination, telephone: 31 (0) 412 – 662964 or send an e-mail to the e-mail address mentioned below. If you are interested please send your letter of application, CV and study results to [2].