Computational Tools: Modelling Multi-molecular Assemblies and Protein Design

Date: 02-Sep-2012 1:00 CEST to -

Contact: Gideon Schreiber


An Instruct funded course

2nd – 6th September 2012
Registration deadline is July, 15th 2012
For registration details please contact:
Natasha Gruber - Course Secretary

Course Overview:

The goal of the workshop is to introduce the participants to state of the art computational methods (algorithms) for the following:

1.      Modeling of macromolecular assemblies based on experimental information obtained from various sources. This includes docking and the assembly of large macromolecular structures.

2.      Learning to use the Rosetta macromolecular modeling suite with a focus on the design of molecular recognition.

3.      Learn how to use Proteopedia to create WEB pages of macromolecular structures and their functions.

Participants are encouraged to bring their own scientific problems related to the course subject, which will be analyzed during the course.

Course content

Part 1: Assembly of macromolecular structures based on experimental datasuch as X-ray crystallography, NMR, Electron Microscopy and cross-linking data. The presentation and analysis of the various methodologies will be followed by hands-on modeling sessions, where the participants will perform the modeling using the servers accessible from the Tel Aviv University INSTRUCT hub.

Day 1: Protein-protein docking -  the PatchDock, FiberDock, Consurf servers.

Day 2: Modeling of multi-molecular assemblies of symmetric proteins – SymmDock, Symmetric MultiFit.

Modeling of (non necessarily symmetric) multi-molecular assemblies – CombDock, MultiFit.

Day 3: Half-day, apply the knowledge gained during the first two days to generate models of real life-protein complexes, desirable of structures suggested by the users. The second half of the day will be used to visit Jerusalem.

Part 2: Usingthe Rosetta macromolecular modeling suite

Day 4: The Rosetta macromolecular modeling suite is being developed as a general platform for prediction and design of biological macromolecules and their assemblies. We will review recent progress in protein design using the Rosetta modeling package with a focus on the design of molecular recognition. Following this a hands-on session devoted to learning how to use Rosetta in various design tasks involving residue substitutions and conformational flexibility as well as how to use Rosetta to analyze binding energy and strain. Participants will be encouraged to tackle systems of relevance to their own research.

Part 3:Learn how to use Proteopedia

Day 5: How to use Proteopedia as a viewerto view structure/function information.

How to edit Proteopedia pages, including text and figures.

Adding images (uploading, and syntax).

Adding an applet (syntax, parameters, help page).

Adding a scene including detailed explanation of the scene authoring tools.

Learn how to use extra functions and how to use proteopedia for presentations or as supplementary material for articles.

Use your own structures or macromolecules of interest and prepare a proteopedia page.


Course Tutors:Prof. Haim Wolfson, Tel-Aviv University

Dr. Jaime Prilusky, Weizmann Institute of Science

Dr. Sarel Fleishman, Weizmann Institute of Science