Počítačové modelování biomolekul
- MetaCentrum (Czech HPC clusters)
- Chimera (Faculty HPC cluster)
- Databases (PDB, Uniprot, PubChem)
- Visualization (UCSF Chimera, VMD, PyMol)
- AI (AlphaFold3, Boltz2 [JMCH], Protenix v2, ESMFold2, BoltzGen, Generative SNUPI)
- Docking (AutoGrow4, AutoDock Vina, DockingPie, CHARMM-gui, BFEE-Docking)
- Molecular Dynamics (CHARMM-gui, OpenMM, GROMACS, AMBER, NAMD)
- Free energy (SMD, US, Metadynamics, ABF, FEP, TI, BFEE3)
- Forcefields (CHARMM, AMBER, Drude, AMOEBA, ECC vs. NBFIX, Martini, PACE, ML)
- MLMM (CHARMM-gui)
- QMMM (CHARMM-gui)
- QM (ORCA, Gaussian, PySCF)
- Parametrization (CGenFF, OpenFF, ffTK, FFParam)
- Biomolecules (Nucleic Acids, Proteins, Membranes)
- Experimental methods
- Lexicon
Nabídka bakalářské či diplomové práce:
