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BImBS 2019 - BioInformatics meets BioSimulations in protein and DNA studies: from theory to practice

Location : Università della Svizzera italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
October 5, 2019 – October 12, 2019


The school is co-organized with the COST Action MuTaLig. The COST action will support 30 selected applicants to partially cover their travel and living expenses. The selection of the COST supported trainees will be carried out by the a Scientific Commission composed by four members of the COST Action, involved in computational research activities. The grant will be sent only after following the training school, according to the rules of the COST Vademecum (Part B).

Computer science plays an ever more central role in our daylife and scientific research. The continuous improvement of simulative algorithms, software and hardware has opened unprecedented routes in biology [1-3]. Currently, people learn bioinformatics and biosimulations techniques in a “do-it-yourself” manner, while the communication between the experts of the different disciplines would favor translational expertise and the fast growth of well-trained scientists.
The BImBS school is designed to meet these requirements posing at the interface of the bioinformatics and biosimulations communities in which researchers often work on thematically related topics but are not prepared to communicate and understand each to the other. The aim of our school is to unveil potential synergies stimulating the cross-talking between the two communities, which is fundamental specially in the education of young scientists.
From the technical point of view, the BImBS school introduces to the theory and practice of some of the most widely used bioinformatics and biosimulations techniques. In detail, the BImBS school deals with:

– Bioinformatics methods applied to structural biology [4-8] and drug design [10-12];

– Biosimulations based on atomistic molecular dynamics (MD) [13-16], multiscale techniques [17-19] and free-energy calculations [20-25].

The BImBS school is a unique event in which apparently different expertise is combined, however preserving a deep analysis of the techniques presented and also paying attention to bridge the gap between computations and experiments.  Lecturers’ expertise covers the following four areas:

1) Bioinformatics for sequence analyses: protein and nucleic acid secondary structure prediction, pattern recognitions, phylogenetic analysis, functional prediction;

2) Structural bioinformatics: homology modelling, protein-ligand docking, receptor-based virtual screening, protein-protein docking;

3) MD simulations: atomistic MD simulations on protein and DNA, Markov state models, experimentally optimized MD simulations;

4) Enhanced sampling and free-energy calculations: free-energy perturbation, metadynamics, umbrella sampling, replica exchange, coarse-grained simulations;

The BImBS school program consists of 8 days, each organized in a morning theoretical session that covers 2 themes, followed by a noon practical session in which the participants can reproduce part of the studies presented in the morning. Particular attention is paid to the practical session as it represents a unique opportunity for the attendees to i) get a deep understanding of each presented technique, ii) acquire basic skills to use the methodology, and iii) solve technical issues that are typically encountered.

The BImBS school is expected to provide an holistic picture of the possible applications of the state-of-the-art techniques in bioinformatics and biosimulations contributing to the formation of young researchers in the resolution of problems that might require cross-disciplinary preparation.
In order to give voice to the young participants and favour their interaction with the senior speakers, a poster session will be organised on day 6 with a competition for the best poster presentation. An oral session of 90 minutes composed by 6 mini-talks of 15 min each is also planned for the best abstracts submitted by the attendees.

The BImBS school is directed to PhD students and postdoctoral scientists interested in bioinformatics and MD simulations. Skills in programming languages are not required, while basic knowledge of linux/unix systems and molecular graphics tools is needed. Applicants with previous experience in one of the presented techniques will have priority.
As technical note, the training material will be shared through the CECAM website. The required infrastructure, in terms of computers and software, will be made available by the host Institution USI Lugano and the organisers.



1. Lacy, M.E. Missing the point. Nature 351, 434 (1991).
2. Gershon, D. Bioinformatics in a post-genomics age. Nature 389, 417-418 (1997).
3. Di Ventura, B. et al. From in vivo to in silico biology and back. Nature 443, 527-522 (2006).
4. Chatzou, M. et al. Multiple sequence alignment modeling: methods and applications. Brief Bioinform. 17, 1009-1023 (2016). 
5. Furnham, N. et al. Current challenges in genome annotation through structural biology and bioinformatics. Curr. Opin. Struct. Biol. 22, 594-601 (2012).
6. Krallinger, M. et al. Information retrieval and text mining technologies for chemistry. Chem. Rev. 117, 7673-7761 (2017).
7. Schneidman-Duhovny, D. et al. Uncertainty in integrative structural modeling. Curr. Opin. Struct. Biol. 28, 96-104 (2014).
8. Schmidt, T. et al. Modelling three-dimensional protein structures for applications in drug design. Drug. Discov. Today 19, 890-897 (2014). 
9. Irwin, J. J. & Shoichet, B. K. Docking Screens for Novel Ligands Conferring New Biology. J. Med. Chem. 59, 4103-4120 (2016).
10. Kufareva, I. et al. Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr. Top. Med. Chem. 12, 1869-1882 (2012). 
11. Abel, R. et al. Accelerating drug discovery through tight integration of expert molecular design and predictive scoring. Curr. Opin. Struct. Biol. 43, 38-44 (2017).
12. Xue, L. C. et al. Computational prediction of protein interfaces: A review of data driven methods. FEBS Lett. 589, 3516-3526 (2015).
13. Klepeis, J. L. et al. Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struct Biol. 19, 120-127 (2009).
14. Hospital, A. et al. Molecular dynamics simulations: advances and applications. Adv. Appl. Bioinform. Chem. 8, 37-47 (2015).
15. Chodera, J. D. & Noé, F. Markov state models of biomolecular conformational dynamics. Curr. Opin. Struct. Biol. 25, 135-144 (2014).
16. Stelzl, L. S. & Hummer, G. Kinetics from replica exchange molecular dynamics simulations. J. Chem. Theory Comput. ASAP (2017).
17. Ingólfsson, H. I. et al. Computational ‘microscopy’ of cellular membranes. J. Cell Sci. 129, 257-268 (2016). 
18. Dama, J. F. et al. The theory of ultra-coarse-graining. 1. General principles. J. Chem. Theory Comput. 9, 2466-2480 (2013).
19. Chavent, M. et al. Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale. Curr. Opin. Struct. Biol. 40, 8-16 (2016). 
20. Wang, L et al. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. J. Am. Chem. Soc. 137, 2695-2703 (2015).
21. Troussicot, L. et al. Funnel-metadynamics and solution NMR to estimate protein-ligand affinities. J. Am. Chem. Soc. 137, 1273-1281 (2015).
22. Limongelli, V. et al. Funnel metadynamics as accurate binding free-energy method. Proc. Natl. Acad. Sci. U.S.A. 110, 6358-6363 (2013). 
23. Tiwary, P. et al. Kinetics of protein-ligand unbinding: predicting pathways, rates, and rate-limiting steps. Proc. Natl. Acad. Sci. U.S.A. 112, 386-391 (2015).
24. Domański, J. et al. Convergence and sampling in determining free energy landscapes for membrane protein association. J. Phys. Chem. B. 121, 3364-3375 (2017).
25. Jo, S. et al Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations. J. Phys. Chem. B 120, 8733-8742 (2016).


Jiangning Song (Monash University)


Luca Monticelli (CNRS, University of Lyon)


Bert de Groot (Max Planck Institute for Biophysical Chemistry, Göttingen)
Helmut Grubmüller (Max Planck Institute for Biophysical Chemistry, Göttingen)
Andrei LUPAS (Department of Protein Evolution, Max Planck Institute for Developmental Biology)


Stefano Alcaro (University of Catanzaro)
Rita Casadio (University of Bologna)
Gianni Cesareni (University of Rome Tor Vergata)

The Netherlands

Alexandre Bonvin (Utrecht University)


Modesto Orozco (University of Barcelona and Institute for Research in Biomedicine)
Alfonso Valencia (Barcelona Supercomputing Center, Spain)

United Kingdom

David Wales (University of Cambridge)


Ruben Abagyan (University of California San Diego and Molsoft)
Gregory Voth (University of Chicago)

Saturday October 5thDay 1


• 08:45 to 09:00 – Registration

• 09:00 to 09:15 – Welcome and Introduction

Bioinformatics for Sequence Analysis and Structure Prediction

09:15 to 10:45 – Andrei N. Lupas: From Sequence to Structure – Deducing Structural Features of Proteins from their Sequences

• 10:45 to 11:15 – Coffee Break

• 11:15 to 12:45 – Gianni Cesareni: The Cell Interaction Network, Physical and Causal Interaction between Proteins

• 12:45 to 14:00 – Lunch

• 14:00 to 16:00 – Exercises

• 16:00 to 16:30 – Coffee Break

• 16:30 to 18:30 – Exercises

Sunday October 6th – Day 2

Bioinformatics for Sequence Analysis and Structure Prediction

• 09:00 to 10:30 – Rita Casadio: Transfer of Knowledge for Structural and Functional Annotation of Protein Sequence

• 10:30 to 11:00 – Coffee Break

Ligand-protein Docking

• 11:00 to 12:30 – Ruben Abagyan: Discovering, Designing or Screening for a Specific Multi-Target Profile of a Small Molecule

• 12:30 to 14:00 – Lunch

• 14:00 to 16:00 – Exercises

• 16:00 to 16:30 – Coffee Break

• 16:30 to 18:30 – Exercises

• 18:30 – Social Aperitif

Monday October 7th – Day 3

Bioinformatics for Personalised Medicine

• 09:00 to 10:30 – Alfonso Valencia: Cell Level Simulations

• 10:30 to 11:00 – Coffee Break

Protein-protein Docking

• 11:00 to 12:30 – Alexandre Bonvin: Integrative Modelling of Biomolecular Complexes

• 12:30 to 14:00 – Lunch

• 14:00 to 16:00 – Exercises

• 16:00 to 16:30 – Coffee Break

• 16:30 to 18:30 – Exercises

Tuesday October 8th – Day 4

Atomistic Molecular Dynamics (MD) Simulations

• 09:00 to 10:30 – Modesto Orozco: Multiscale Simulations of DNA

• 10:30 to 11:00 – Coffee Break

Free Energy Calculations

• 11:00 to 12:30 – Bert L. de Groot: Alchemical Free Energy Calculations

• 12:30 to 14:00 – Lunch

• 14:00 to 16:00 – Exercises

• 16:00 to 16:30 – Coffee Break

• 16:30 to 18:30 – Exercises

Wednesday October 9th – Day 5

Free Energy Calculations

• 09:00 to 10:30 – David Wales: Exploring Energy Landscapes: From Molecules to Nanodevices

• 10:30 to 11:00 – Coffee Break

• 12:00 to 12:30 – Vittorio Limongelli: FMAP: the Funnel-Metadynamics Automated Protocol for Ligand Binding Free-Energy Calculations

• 12:30 to 14:00 – Lunch

• 14:00 to 16:00 – Exercises

• 16:00 to 16:30 – Coffee Break

• 16:30 to 18:30 – Exercises

Thursday October 10th – Day 6

COST Action

• 09:00 to 09:45 – COST Action – Stefano Alcaro: The MTDD approach and the Chemotheca tool in the MuTaLig COST Action

• 09:45 to 10:30 – Jiangning Song: Harnessing the Power of Machine-Learning Techniques to Address Biomedical Classifications Problems 

• 10:30 to 11:00 – Coffee Break

• 11:00 to 11:30 – CSCS – Victor Holanda Rusu

• 11:30 to 13:00 – Short Oral Communications

• 12:30 to 14:00 – Lunch

• 14:00 to 16:00 – Poster Session

• 16:30 to 18.30 – Visit @ CSCS

• 20:00 to 23:00 – Social Dinner

Friday October 11th – Day 7

Atomistic MD Simulations

• 09:00 to 10:30 – Helmut Grubmüller: Atomistic Simulation of Biomolecular Function

• 10:30 to 11:00 – Coffee Break

Coarse-grained Simulations

• 11:00 to 12:30 – Luca Monticelli: The MARTINI Coarse-Grained Force Field: Principles and Applications

• 12:30 to 14:00 – Lunch

• 14:00 to 16:30 – Exercises

• 16:00 to 16:30 – Coffee Break

• 16:30 to 18:30 – Exercises

Saturday October 12th – Day 8

Coarse-Grained Simulations

• 09:00 to 10:30 – Gregory A. Voth: Systematic Coarse-Graining: Fundamentals and Applications

• 10:30 to 11:00 – Coffee Break

• 11:00 to 12:30 – Exercises

• 12:30 to 13:00 – Concluding Remarks

To apply: Click here

To submit an abstract: Click here

The booklet can be found here