Czech Society for Structural Biology
Česká společnost pro strukturní biologii



The Czech Society
for Structural Biology
(Česká společnost
pro strukturní biologii

Videnska 1083
CZ-142 20 Prague
Czech Republic

CSSB@structbio.org
VAT number: 0022869433
account num.: 2300076583/2010
IBAN: CZ2820100000002300076583
SWIFT/BIC: FIOBCZPPXXX

Instruct-ERIC workshop on Computational Approaches in Integrative Structural Biology - Preliminary program

Preliminary program of Instruct-ERIC workshop on Computational Approaches in Integrative Structural Biology:

Instruct‐ERIC workshop
Computational approaches in integration of structural biology techniques
Institute of Biotechnology of the Czech Academy of Sciences, Research centre Biocev, Prumyslova 595
Vestec near Prague, Czech Republic


Preliminary programme (times and details may change)

Tuesday, October 8 2019

~ 8:30    Arrival, coffee, instructions, meeting others
9:00‐9:10    Welcome, Overview of structural biology techniques and opportunities in Biocev, Jan Dohnalek, IBT Biocev
9:10‐9:40    Small angle X-ray and neutron scattering - computational aspects in integration of structural data, Haydyn Mertens, EMBL Hamburg
9:40‐10:00    Diffraction techniques - focus on data processing and computational aspects, Jan Stransky, IBT Biocev
10:00‐10:20    Constraint-driven protein structure modeling, Nikolay V. Dokholyan, Penn State College of Medicine
10:20‐10:40    Biophysical techniques for the structural and functional biomolecules characterisation, Tatsiana Charnavets, IBT Biocev
10:40‐11:00    Coffee break w. snack
11:00‐11:30    CryoEM - update and focus on computational approaches, Daniel Nemecek, Thermofisher
11:30‐12:00    CryoEM model building and other tools in Phenix, Paul Adams, LBNL, To be confirmed
12:00‐12:30    Macromolecular docking, HADDOCK and related, applications, Jorge Roel, Bonvin lab
12:30‐13:00    Computational tools for integration of structural data, Ignacia Echeverria, Sali lab, UCSF
13:00‐14:00    Lunch (local canteen)
Introduction to selected techniques available in Biocev, at instruments, with details
14:00‐15:30    Four groups - 45 min rotation - four techniques, at instruments, experimental details, sample manipulation, data processing and type of output. Mass spec, X-ray diffraction, SAXS, CD or DLS or nanoDSF (One person covers two techniques during this session).
15:30‐16:00    Coffee break w. snack
16:00‐17:30    Four groups - 45 min rotation - four techniques, at instruments, experimental details, sample manipulation, data processing and type of output. Mass spec, X-ray diffraction, SAXS, CD or DLS or nanoDSF (One participant covers the two remaining techniques during this session).
19:00    Dinner in town

Wednesday, October 9 2019

~ 8:30 Arrival, coffee
Data integration, examples, user cases - lessons and know how to learn
9:00‐10:00 Structure and mechanism of DNA delivery of gene transfer agent studied by cryo-EM, Pavel Plevka, CEITEC MU
10:00‐10:30 Structural biology of 14-3-3 protein complexes based on combination of high and low resolution approaches, Tomas Obsil, Faculty of Science, Charles University Prague
10:30‐11:00 A glimpse into the structure-function relationship of the mysterious RNA polymerase effector - HelD, Tomas Koval, IBT Biocev
11:00‐11:30 Coffee break w. snack
11:30‐12:00 Integrative structural characterization of human histone deacetylase 6, Cyril Barinka, IBT Biocev
12:00‐12:30 Integrative approach for structural analysis of flexible protein complexes, Evzen Boura, IOCB Prague
12:30‐13:00 Coot as a tool for integration of structural data, To be confirmed
13:00‐14:00 Lunch (local canteen)
Workshops on data processing and interpretation
14:00‐15:00 Data processing and interpretation on laptops, Xray-CryoEM, refinement included, To be confirmed
15:00‐15:15 Short break
15:15‐16:15 Data processing and interpretation on laptops, SAXS-X-ray-Cryo-EM
16:15‐16:30 Short break
16:30‐17:30 MS data processing and interpretation on laptops, StavroX, MeroX
19:00 .... Workshop dinner at Villa Lanna

Thursday, October 10 2019

~ 9:00 Arrival, coffee
9:15‐10:00 Native MS in biophysical and structural characterization of protein complexes, Charlotte Uetrecht, Leibniz Institute for Experimental Virology, Hamburg
10:10‐10:30 3D-Bioinfo: ELIXIR initiative in structural bioinformatics and its integration into structural biology, Bohdan Schneider, IBT Biocev
10:30‐11:00 Coffee break
11:00‐11:30 CCP4MG for analysis and presentation of structural results, Stuart McNicholas, University of York
11:30‐12:00 Validation with focus on combination of techniques or their specific needs, deposition etc., To be confirmed
12:00‐13:00 Lunch (local canteen) + coffee and goodies
13:10‐14:00 HADDOCK/DISVIS tutorial, Jorge Roel, Bonvin lab, Utrecht University, 90 minutes
14:00‐14:15 Short coffee break
14:00‐15:30 Workshops continued a mix of parallel sessions - choose your topic:
CCP4MG for analysis and presentation of structural results, Stuart McNicholas, University of York, To be confirmed
Integrative structural determination using IMP: Applications and examples, Ignacia Echeverria, Sali lab, UCSF, 90 minutes
May be other?
15:30‐15:40 Workshop close