Computational Molecular BioMedicine - WiSe 2023/2024

Wahlfach (Q1+Q2) der Medizinischen Fakultät der HHU Düsseldorf

Dozentin:  Dr. Mercedes Alfonso-Prieto




Tag: Mittwoch

Zeit: 15:00 – 16:30 Uhr

Rhythmus: wöch. 11.10.2023 bis 07.02.2024   (Vorlesung fällt am 01.11.2023 aus!)

Raum: Hörsaal Frauenklinik (Geb.  14.75)

Vorlesungssprache: Englisch


Teilnahme ist ausreichend.

Die Prüfung ist nicht obligatorisch, aber nach Absprache möglich (wenn Sie ein benotetes Wahlfach wünschen).

Molecular BioMedicine 

is a broad field where physical, chemical, biological and medical techniques are used to identify the underlying causes and mechanisms of disease at the genetic and molecular level, as well as to develop molecular-based strategies for diagnosis and treatment. 

From the seminal paper of Linus Pauling on sickle cell anemia to the recent genomic studies on gliomas, the Molecular BioMedicine field has been expanding, thanks in part to the development of computational methods. 

This course (in English) will introduce basic concepts of Computational Molecular BioMedicine, covering topics such as bioinformatics, structural modeling, molecular docking, drug design and molecular dynamics simulations. 

In addition, it will present freely available computational tools and webservers commonly used in the field. 

The theoretical concepts will be exemplified by case studies, mostly drawn from Neuromedicine. 

* Preliminary Literature & Documentation *

Relevant literature and documentation will be provided, as well as the slides of the lectures.

Some general links can be found below:

 - Molecular Medicine - To be or not to be (Link)

  - Protein Data Bank: Molecule of the Month & Educational Resources.

  - VMD: Gallery of Images & Movies.

  - "Molecular Modelling: principles and applications". Andrew R. Leach, Prentice Hall (2001).

  - "Molecular Modeling and Simulation: an interdisciplinary guide". Tamar Schlick, Springer (2010).

  - "From Protein Structure to Function with Bioinformatics". Daniel J. Ridgen, Springer (2017).

* Rough Syllabus *

Stand: Juni 2022

01. Introduction to Molecular Biomedicine

Links:  Molecular Medicine in Wikipedia

Image credit: TCBG at Univ. of Illinois Urbana-Champaign

02. Structure of biomolecules

Links: Protein Data Bank and PDBSum

Image credit: Howarth's alphabet

03.  Protein-Ligand Interactions

Links: DrugBank, PubChem and ZINC.

Image credit: PDB-101

04. Methods for Structural Determination

Links:  SwissModel and GOMoDo webservers; AlphaFold Protein Structure database

Image credit: PDB-101

05. Homology Modeling Examples

Links:  SwissModel and GOMoDo webservers

Image credit: University of Lausanne

06. Molecular Docking: Protein-Ligand

Links: HADDOCK and GOMoDo  webservers 

Image credit: Wikipedia

07. Protein-Ligand Docking Examples

Links: GPCRdb and GOMoDo

Image credit: GOMoDo

08. Drug Design

Links: Drug Design Workshop

Image credit: Röhrig et al. J. Med. Chem. (2015)

09. Molecular docking: Protein-Protein

Links: HADDOCK webserver

Image credit: ZIB at University of Saarland

10. Disease-linked Mutations 

Links: OMIM and dSysMap databases

Links:  Elaspic , MutaBind and DynaMut webservers

Image credit: NIH-National Cancer Institute

11. Molecular Dynamics: Basics

Links: Folding@home and GPUGrid; Molecular Dynamics Movies from the TCBG at UIUC

Image credit: Beckstein Lab

12. Molecular Dynamics & Disease-Linked Mutations

Image credit: Molecular Dynamics Movies from the TCBG at UIUC

13. Molecular Dynamics & Drug Design

Image credit: Iglesias et al. WIRES Comput. Molec. Sci. (2018)

14. Molecular Dynamics: Online Resources

Links:  MoDEL, MemProtMD, GPCRmd, Dynameomics and BigNASim; MDWeb and CHARMM-GUI.

Image credit: Beckstein Lab