Molecular modelling techniques in the quest of novel lead compounds

    Atilla Akdemir, PhD


Brief Course Contents:

In the drug discovery process a huge number of compounds are being synthesized (>>10.000) in the attempt to identify structurally novel compounds with activity against a predefined target protein. Many of these compounds fail due to lack of affinity and activity against the target protein, lack of selectivity, unfavourable pharmacokinetic properties and toxicity problems. The correct application of molecular modelling techniques in the drug discovery process will steer the synthesis efforts to obtain higher quality leads with less synthetic efforts.

This course will discuss the correct application of virtual screening methods from “ligand preparation” to “selection of compounds for synthesis” in the drug discovery process:

  • preparation of virtual compound libraries
  • selection and preparation of protein crystal structures
  • preparation and validation of homology models
  • pharmacophore screening
  • set-up, validation and application of docking protocols
  • analysis of docking results
  • molecular dynamics simulations
  • de novo ligand design procedures
  • suggestion of compounds for synthesis


Course duration: 3 hours theory and 3 hours applications.

Course programme: The course programme will be announced later

Number of attendants: 25 students (preferably MSc – PhD students- Assist. Proffessors)

Course language: The course will be in English.

Who should attend: This course is mainly intended for postgraduate students (MSc – PhD students, Assist. Proffessors), who would like to use molecular modelling techniques in their research projects aiming at ligand design.

Course attendants are required to bring their own laptops to the course! MOE trial licenses will be provided before the start of the course. Please check the system requirements for your laptops:


Course fee: 100 Euro

Fatma Albayrak
Phone: 0541 6734593


Bank Account Information

Bank Account Name

Kimyagerler Derneği İktisadi İşletmesi

Bank Name

Türkiye İş Bankası

Bank Branch

Perpa Şubesi, İstanbul

Branch Code


Swift (BIC) Code


IBAN (for TL)

TR74 0006 4000 0011 1880 5904 45

Account number (for TL)


IBAN (for USD)

TR05 0006 4000 0021 1880 2935 04

Account number (for USD)


IBAN (for EUR)

TR85 0006 4000 0021 1880 2935 19

Account number (for EUR)


Bank Adress

Darülaceze Cad. Perpa İş merkezi Kat 8 No: 1211 Perpa Okmeydanı 34384, Şişli, İstanbul

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