Docking and Introductory Molecular Dynamics

Friday, 24 November 2017, 09:00
Docking and Introductory Molecular Dynamics

Bio-molecular Simulation School

Module I: Docking and Introductory Molecular Dynamics

Course type:

Hands-on Practical course

Course Duration:

2 days

Course Location:

Nawah Scientific: 7094, Street 17 off Street 9, Almokattam Cairo.

Course offered on:

Friday 24-11-2017 (9:00am - 5:00pm)

Saturday 25-11-2017 (9:00am - 5:00pm)  

Target audience:

Students and post-grad students

Course instructors:

Dr. Ahmed Taha Ayoub

Dr. Ahmed graduated from the Faculty of Pharmacy at the German University in Cairo and pursued his PhD at the University of Alberta in the field of theoretical and computational chemistry and computer-aided drug design. With his 9 year experience in teaching and research related to computational chemistry, he is currently an assistant professor at the medicinal chemistry department at Heliopolis University.

Dr. Mohamed Alaraby Salem

Dr. Mohamed is a highest-honour graduate from the faculty of pharmacy and biotechnology, GUC. In 2016, he completed his PhD at the University of Alberta in the field of computational chemistry. Since then, he has been working as a lecturer of medicinal chemistry and drug design at the MSA University. He contributes to several workshops and events to teach the concepts of computer-aided drug design.

Module Summary:

Docking is a computational chemistry tool used frequently to predict the binding mode of a small molecule within a binding site or to screen a virtual library against a certain target. It is usually supplemented with molecular dynamics simulations which utilizes the formalism of statistical mechanics to calculate ensemble properties of the system of interest. With these two methodologies in hand, a computer can be used to save a lot of time, effort and money and sometimes even predict molecular properties that are impossible to measure in the lab.

In this module of the course we will touch base on the theoretical basis of both algorithms and apply them in hands-on exercises supervised by experts in the field. The exercises will focus on the strength and weakness of each protocol and the participants will assess the utility and accuracy of each method.

Watch this introductory video:


  1. Lecture manuals and notes are provided.
  2. Each participant needs to bring his/her own laptop. 
  3. The maximum number of attendees is 15.


1. Log in to your account on our website, or create a new account
2. From your personal control panel, choose this course and register
3. Registration will be only confirmed upon payment. 


1. Using Vodafone cash: please transfer the course fees to (01064488216)
2. Pay on site: please visit our labs from Saturday-Thursday, 10 am - 5 pm.


Sign in to check course timings and register

Price: 600 L.E.