XІІ INTERNATIONAL SUMMER SCHOOL-CONFERENCE
#(Oleksandr V. Savytskyi, Institute of Molecular Biology and Genetics NASU)
–Review–
http://biomolecula.ru/insilico
–Additional software–
http://www.putty.org/
http://winscp.net/eng/docs/lang:ru
–Applied software–
[Molecular modeling]
http://salilab.org/modeller/
http://swissmodel.expasy.org/
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
http://robetta.bakerlab.org/
[Molecular dynamics]
http://www.gromacs.org/
http://www.ks.uiuc.edu/Research/namd/
[Molecular Visualisation]
http://www.pymol.org/
http://www.cgl.ucsf.edu/chimera/
http://www.ks.uiuc.edu/Research/vmd/
http://qutemol.sourceforge.net/
–References–
http://biochem.wisc.edu/sites/default/files/facilities/bcrf/tutorials/MODELLER/modeller_i_introduction.pdf
https://biochem.wisc.edu/sites/default/files/facilities/bcrf/tutorials/MODELLER/chimera_ii_modeller_gui.pdf
http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-tutorial.pdf
–Computational resources–
[GRID]
http://ung.in.ua/
http://infrastructure.kiev.ua/
http://voms.grid.org.ua/voms/
http://ca.ugrid.org/index.php
http://www.nordugrid.org/
http://kb.iu.edu/d/avmy
[Virtual organizations]
http://moldyngrid.org/main.php
http://www.wenmr.eu/
________
Workflow
- Install Portable Firefox https://portableapps.com/apps/internet/firefox_portable
- Request personal certificate from KNU Testbed CA: https://testbed.univ.kiev.ua/ca_request.php (choose MolDynGrid in department dropdown list)
- Report to trainer you have sent certificate request and wait for request to be signed. Check certificate availability here: https://testbed.univ.kiev.ua/ca_valids.php
- Request VO MolDynGrid membership here: https://voms.grid.org.ua/voms/?vo=moldyngrid&action=register
- Report to trainer you have sent membership request to be confirmed and added to /moldyngrid/edu group.
- Now you are able to access MolDynGrid EDU WebShell: https://moldyngrid.org/edushell/