eSSENCE workshop on macromolecular structure and dynamics

3-5 June 2013, Uppsala University, Sweden


E-science as applied to macromolecular structure and dynamics means tightening the connection between computation and experiments, and improving infrastructure for in silico studies. This is a 3-day workshop where leading experts on macromolecular modeling meet and present a series of talks. The list of speakers combines researchers from Sweden (many of them being part of the eSSENCE network) as well as from other countries. Key topics of interest are computational biology, drug discovery, high performance computing, and algorithm development. The workshop will be divided into a first part of conferences and talks (2 days) followed by hands-on sessions (1 full day) to train the attendees on cutting-edge computational tools. This workshop is mainly addressed to degree and postdoctoral scholars (either computational or experimental) working in the areas of molecular biology, biochemistry, biophysics or chemical biology, as well as staff scientists as an advanced training course.

Advance registration (here) is required, but there is no charge for this. 

Venue:  Talks will be held in lecture hall B42, Biomedical Center, Husargatan 3, Uppsala.  Tutorials will be held in smaller rooms to be determined.

Call for abstracts (here)  for oral presentations closes May 3, 2013.


Recommended hotels are:

This is convenient, just across from the train station.  It is a full service hotel with 24 hour concierge.  When making your reservation, specify that you are visiting Uppsala University for this workshop and request the discounted rate.

This is a brand-new hotel (built in March) which is across the street from Hotel Svava and thus equally convenient, but cheaper.  Assemble or cook your own breakfast from a well stocked fridge, pantry, and espresso machine, included in your room rate.  Front desk is staffed 24 hours.  Mention our workshop at Uppsala University and ask for the 15% discounted rate.

This place is just a few blocks farther away. It is a sister hotel to Hotell Centralstation, and similarly priced so a great option if the latter is full. Breakfast arrangement and workshop discount is the same as for Hotell Centralstation.   For Kungsängstorg, however, you should watch out for the restricted front desk hours.   


Uppsala is about 15 minutes from Arlanda airport by train, or a little under an hour (and cheaper) by bus.  You can buy tickets at the information desk at the airport, after you exit customs. 

We will lead a group on foot from the hotel Svava (see below). Walking even on your own is not particularly complicated, and should take about 35 minutes, though you should give yourself more time the first time. Here is a university overview map, and here is a closeup of the area around BMC.

Otherwise buses 1,8,20,110,111, and 115 leave from the train station (Centralstationen, on driveway between Kungsgatan and the station) and stop in front of BMC (Uppsala Science Park). Ask the operator when boarding, Centralstationen is organized in a somewhat counterintuitive manner. You can pay on board with a credit card if it has a chip (30SEK per ride) or buy a bus card in Centralstationen (75 SEK refundable deposit, 16 SEK per ride). The first morning, you may want to have the front desk call a taxi for you.

Lastly, here is building plan for BMC showing entrance A11 (where you can enter the building) and room B42 (where the talks are held).

Contact Samuel Flores at samuel.flores _at_, +46 70-600 04 64  or Hugo Gutierrez de Terán at hugo.gutierrez _at_ . For speaker lunches and dinners, contact Daniel Dourado (+46 0736511614).

Sweden extends its warm welcome to the delegates from the United States, Spain, France, UK, Germany, Belgium, Ukraine, and other countries.

Final Program

Invited speaker

Selected oral presentation

Sunday 2 June

18:30 - Welcome Dinner for Invited Speakers (meeting at Svava Hotel Lobby)

Monday 3 June

8:00  (Speakers) Meet in lobby of Hotel Svava, walk to BMC (Daniel D. +46 736511614)

A- Membrane Proteins

Chair: Hugo Gutierrez de Terán (UU)

8:45-9:00  Welcome and announcements

9:00-9:40Paolo Carloni, Institute for Advanced Simulation (IAS), Jülich (Germany) “Multi-scale studies of membranes and membrane proteins

9:40-10:20 Jordi Villà-Freixa, University of Vic (Spain) “Globular and membrane proteins modelling for structure-based protein-ligand interactions characterization

10:20-10:40Fika (coffee break)

10:40-11:00Ozge Yoluk (KTH Royal Institute of Technology) “Structural dynamics of Glutamate-Gated Chloride Channel in Presence and Absence of Ligands”

11:00-11:20Lars Boukharta (Uppsala University) “Computational alanine scanning of GPCR-antagonist complex using Free Energy Perturbation”

D- Drug design & chemometrics  

Chair: Johan Åqvist (UU)

11:20-12:00Jens Carlsson, Stockholm University, (Sweden) “Two steps forward and one step back: Successes and failures in structure-based discovery of GPCR ligands

12:00-13:00  Lunch


13:00-13:40Andreas Bender, Cambridge University (UK) “Drug Design Using Bioactivity Databases and Computational Algorithms: From Proteochemometrics to Target Prediction

13:40-14:10 Thomas Caulfield, Mayo Clinic Florida (USA) “IDockMdMD: Induced-fit docking with Maxwell's demon molecular dynamics for improved ligand-receptor optimization”

14:10-14:30David Rodríguez (Stockholm University) “Structural modelling of G Protein-Coupled Receptors: protein, ligand-binding and receptor oligomers”

B- Nucleic Acids  (I)

Chair: Magnus Ullner (LU)  

14:30-15:20Eric Westhof, Université de Strasbourg & CNRS (France) “RNA Architectural Modules, their Detection in RNA Sequences and the assembly of large RNAs”    

15:20-15:50Mark Bathe, Massachusetts Institute of Technology, USA “Computer-aided Engineering of Functional Nucleic Acid Nanostructures

15:35-17:30Fika and poster session

19:00 - Dinner for Oral and Invited Speakers @ Katalin (meeting 18:30 at Svava Hotel Lobby)

Tuesday 4 June

C- Protein-protein interactions

Chair: Iain Moal (BSC)

8:00  (Speakers) Meet in lobby of Hotel Svava, walk to BMC (Daniel D. +46 736511614)

09:00-09:40Mikael Lund, University of Lund (Sweden) “A Coarse Grained Approach to Ion Specific Interactions Between Biomolecules

09:40-10:00 Oleksandr Savytskyi (Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine) “Domain binding interfaces in human tyrosyl-trna synthetase studied by the Hierot technique and molecular dynamics simulations”

10:00-10:20Fika (coffee break)

10:20-11:10Iain Moal, Barcelona Supercomputing Center (Spain) “Structural prediction of protein-protein and protein-RNA complexes

11:10-11:50Joost Schymkowitz, Leuven University (Belgium) “Generating artificial aggregation-associated phenotypes

12:00-13:00  Lunch

B- Nucleic Acids  (II)

Chair: Samuel Flores

13:00-13:40 Magnus Ullner, University of Lund (Sweden) “Questionable Results in the Literature Concerning the Structural Properties of DNA

13:40-14:00Erik Marklund, (University of Oxford) “LacI follows a helical path while sliding along DNA”

14:00-14:20 Nina M. Fischer (Uppsala University) “Elucidating DNA-binding specificities of WRKY transcription factors by molecular dynamics”

14:20-14:40Annalisa Arcella (Institute for Research in Biomedicine, Barcelona, Spain) “Nucleic Acids in the gas phase”

14:40-15:00Christoffer Lind (Uppsala University) “Homology Models and Free Energy Calculations on the Human Mitochondrial Release Factors mtRF1a and mtRF1”

15:00-15:40Lennart Nilsson, Karolinska Institute, (Sweden)

15:40-17:30Fika and poster session

19:00 - Dinner for Invited Speakers

Wednesday 5 June: Hands on sessions

Held in computer lab A6:003 (under Bikupan cafeteria)

9:00-12:00  Workshop GPCR-ModSim (, Hugo Gutiérrez de Terán (UU)

12:00-13:00  Lunch

13:00:16:00  Workshop on MMB (Samuel Flores, UU).  Please bring your laptop with MMB installed (, and do exercise 0 from the tutorial in advance.


Confirmed speakers and instructors:  Jordi Villà-Freixa, Paolo Carloni, Hugo Gutierrez de Terán, Magnus Ullner , Lennart Nilsson,  Mark Bathe, Eric Westhof,  Mikael Lund,  Juan Fernández-Recio, Joost Schymkowitz, Jens Carlsson,  Samuel Flores, Andreas Bender