Syllabus
1) Databases: PDB (proteins), NDB (nucleic acids)
2) Homology modeling: Modeller, Consensus, Fasta
3) Docking: AutoDock, Dock
4) Molecular dynamics: NAMD (mindy)
5) Molecular dynamics: AMBER (sander, pmemd, nmode, leap, antechamber, ptraj)
6) Molecular dynamics: GROMACS, Yasara
7) Analysis: PTRAJ, Carnal, 3DNA, MDTool
8) Visualization: Chimera, VMD + Raster3d
9) Ab initio calculations: Gaussian
10) Ab initio calculations: Gamess, NBO5, WebMO
11) Visualization: Molden, ChemCraft, MolScript, gOpenMol, Molekel
12) Force field parametrization: RESP, Glycam
13) Available hardware: ČR MetaCentrum CoupledClusters LUNA Svět Juelich Barcelona
14) Grid solution for biomolecules.
Annotation
Drug design, searching and visualization of biomolecular structures, sequence similarity searching against nucleic acids and protein databases, alignment of a sequence to be modeled with known structures, homology modeling, docking - the identification of the low-energy binding modes of a small molecule within the active site of a macromolecule, efficient algorithms to search the potential binding modes, molecular dynamics simulations for systems with hundreds to millions of particles, force field parametrization and topology, file creation for unusual molecular system, practical excercises.