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 docking • Multidimensionalparametricstudies • Genom/genome evolution analysis • …
3 Structuralbiology MetaCentrum–Czechgride-Infrastructure
4 Applications MetaCentrum–Czechgride-Infrastructure • Computational chemistry § Amber (bio)molecularsimulations § Gaussian 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, Dalton, 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 software – 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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