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Workshop 20-24/04/2009

Modelling protein-carbohydrate recognition in-silico

supported by:

Organised by the School of Biosciences
in collaboration with the Centre for Parallel Computing

to be held at: 

New Cavendish Campus, University of Westminster, London, UK

April 20th-April 24th 2009

Carbohydrates are important recognition molecules in cancer, cell biology, development and differentiation virology and microbiology. Understanding the physiochemical properties and mechanisms which provide cognate specificity and selectivity in protein-carbohydrate recognition can lead to the design of novel therapies by targeting glycosylation aberrancies resulting from human tissue pathology. Complex carbohydrate molecules which are carried on glycoproteins and glycolipids that are present, within the cell, in secretions and decorate the surface membrane of human tissue are thought to be dynamic in nature and therefore have the ability to occupy multiple conformations in time and space. Hence, a computational approach for developing models for protein-carbohydrate recognition is advantageous as it provides extensive ability to sample different carbohydrate conformations which are limited to some of the more conventional experimental approaches in biology. This approach can help to identify prerequisites in protein based-therapy design and parallel conventional wet laboratory based experimental approaches in vitro or in vivo.

Therefore the School of Biosciences and the Centre for Parallel Computing (CPC) will be hosting a joint introductory training workshop for bioscientists interested in building intuitive models of protein-carbohydrate interactions. The training will be led by

Dr. Ross Walker, SDSC, USA,

Dr. Michael Crowley, NREL, USA and

Dr. Martin Frank, GCRC, Germany.

Dr. Walker and Dr. Crowley are members of the development team for AMBER and CHARMM molecular dynamics packages and Dr. Frank has experience using AutoDock in modeling protein-carbohydrate recognition.

The workshop will train participants on how to use these programs to run in silico experiments. It will also teach bioscientists how to model carbohydrate binding proteins and their ligands on the UK National Grid Service (NGS) to decrease execution times of experiments using a web-based graphical user interface (GUI), which was developed within the framework of the ProSim project supported by the JISC Engage programme. (

Further information about the workshop including the registration page is available at

The deadline for registration is the 19th of March 2009.

For more information contact Dr. Pamela Greenwell (

Final Program:

Instructors: Ross Walker (RW), Michael Crowley (MC), Martin Frank (MF)
Organisers: Babak Afrough (BA), Pamela Greenwell (PG), Tamas Kiss (TK),
Hans Heindl (HH), Gabor Terstyanszky (GT), Noam Weingarten (NW)

(L) = Lecture, (H) = Hands on Tutorial

Day 1 (Monday 20th April 2009)

9:00 - 9:30 Registration.  
9:30 - 9:45 Welcome / Introduction to the Workshop. (L) BA / PG
9:45 - 10:30 Introduction to force fields and molecular dynamics. (Part 1) [print version] (L) RW
10:30 - 11:00 Coffee break.  
11:00 - 11:45 Introduction to force fields and molecular dynamics. (Part 2) [print version] (L) MC
11:45 - 12:15 General overview of molecular dynamics packages. [print version] (L) MC
12:15 - 13:00 Overview of the AMBER package and its programs. [print version] (L) RW
13:00 - 14:00 Lunch.  
14:00 - 15:00 Introduction into the simulation of carbohydrates [print version] (L) MF
15:00 - 15:45 Case Study: Simulations of Cellulase and Cellulosome interactions with Cellulose in support of biofuel research [print version] (L) MC
15:45 - 16:15 Tea  
16:15 - 17:30 Mini-symposium 1 - Opportunity for attendees to present overviews of their work (approx 15 mins per talk)  

Day 2 (Tuesday 21st April 2009)

9:00 - 12:00 Hands-on session 1 - (Introduction to molecular dynamics simulations using AMBER) (H) RW/MC/MF
12:00 - 13:00 Lunch.  
13:00 - 13:30 Setting up a protein carbohydrate complex [print version] (L) MF
13:30 - 15:30 Hands-on session 2 - (Building and simulating a protein/carbohydrate complex) (H) RW/MC/MF
15:30 - 16:00 Tea.  
16:00 - 16:30 Implicit solvent and binding energy calculations using MMPBSA [print version] (L) RW
16:30 - 17:00 Free energy calculations [print version] (L) MC

Day 3 (Wednesday 22nd April 2009)

9:00 - 11:00 Hands-on session 3 - (Analysis of protein/carbohydrate simulations using CAT) (H) RW/MC/MF
11:00 - 11:30 Coffee Break.  
11:30 - 13:00 Hands-on session 4 - (Calculating relative binding free energies for protein/carbohydrate complexes) (H) RW/MC/MF
13:00 - 14:00 Lunch.  
14:00 - 15:30 Hands-on session 4 Contd. - (Calculating relative binding free energies for protein/carbohydrate complexes) (H) RW/MC/MF
15:30 - 16:00 Tea break.  
16:00 - 17:30 Mini-symposium 2 - Opportunity for attendees to present overviews of their work (approx 15 mins per talk)  

Day 4 (Thursday 23rd April 2009)

9:00 - 9:30 Designing a Good Simulation Project [print version] (L) RW
9:30 - 10:30 An introduction to docking using AutoDock [print version] (L) MF
10:30 - 11:00 Coffee Break.  
11:00 - 13:00 Hands-on session 5 - (Using AutoDock with Protein/Carbohydrate complexes) (H) RW/MC/MF
13:00 - 14:00 Lunch  
14:00 - 15:30 Focus Groups / Q & A (L) RW/MC/MF/BA/PG
15:30 - 16:00 Tea Break  
16:00 - 17:30 Opportunity to continue hands-on tutorials (H)  

Day 5 (Friday 24rd April 2009)

09:00 - 10:00
10:00 - 10:30
10:30 - 11:15
11:15 - 12:00
12:00 - 13:00
13:00 - 13:30
13:30 - 15:00              

Grid Computing and User Support (L)
Coffee Break
National Grid Service (NGS) and Users (L)
ProSim: Protein Molecule Simulation on the Grid (D)
e-Infrastructure and e-Researchers: lessons and opportunities from the ENGAGE Initiative (L)
Docking using AutoDock and the NGS PGRADE Portal (H)
                               Lecture slides and practical hand-outs
                               Input files for the workflows
                               Link to the portal for the tutorial

Andrew Richard, NGS

Stephen J Brewer, OMII-UK

Workshop registration form