MetaCentrum–Czechgride-Infrastructure

MetaCentrum . e-Infrastructure for solvingstructural biology research challenges

Jan Kmuníček, Martin Kuba CESNET & ÚVT MU meta.cesnet.cz Content MetaCentrum–Czechgride-Infrastructure

• Structuralbiology • Applications • Support • Newservices

2 Structuralbiology MetaCentrum–Czechgride-Infrastructure

• Engineering of (multi)-enzymaticstructures • QM/MM studies of catalysis • Insight into the binding process • Protein structure prediction • Protein-protein • Multidimensionalparametricstudies • Genom/genome evolution analysis • …

3 Structuralbiology MetaCentrum–Czechgride-Infrastructure

4 Applications MetaCentrum–Czechgride-Infrastructure • § Amber (bio)molecularsimulations § elektronicstructureof molecules § Gamess ab-initioQM calculations § Gromacs moleculardynamics § WIEN2k elektronicstructureof solids

§ NAMD paralleldynamicsof biomolecules § Tinker molecularmechanics/dynamicsof biopolymers § VASP ab-initioQM moleculardynamics § Abinit elektronicstructureof crystals

5 Applications MetaCentrum–Czechgride-Infrastructure

• Structuralbiology/bioinformatics § X-Plor 3D structureof macromolecules § Queen evaluation ofNMR parameters § MrBayes estimation of fylogeny § CS-Rosettagenerationof protein structures

• Userapplications – installed by individual users themselves § DL-POLY, , MPQC, .... x

6 Applications MetaCentrum–Czechgride-Infrastructure Computationstime(usertime, last year)

7 Applications MetaCentrum–Czechgride-Infrastructure

• Basicconcept – end user utilizes an applicationsoftware (OpenSourceorcommercial) – based on the request, according to licence and benefit for Meta users we help install and operate user – MetaCentrum participation at costs needed forlicenses purchase to cover (if possible) the whole MetaCentrum

8 Support MetaCentrum–Czechgride-Infrastructure

• Formsof application support – programs installation and update – request to RT • Development of user interfaces – CharonGUI • Solutions „tailored to users needs“ – Multipleligandtrajectorydocking • Testingof trial versions – program ADF

9 Support MetaCentrum–Czechgride-Infrastructure

10 Support MetaCentrum–Czechgride-Infrastructure

11 Newservices MetaCentrum–Czechgride-Infrastructure

• Long-term aim – user driven infrastructure • Means to reach the aim – individualizationof computational environment utilizing virtualization

12 New services MetaCentrum–Czechgride-Infrastructure

• Benefits of virtualization for users – support for new types of utilization – support of preemption § suspension of virtual machine to allow run of high priority computational jobs – user customizable environment § up to own operation system – extremely easier resources management

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