| Level Label |
Task |
| I. |
Small Organic Molecules (<100 heavy atoms) |
|
Determination of reasonble 3D-geometry from SMILES including major conformers, tautomers, and protonation states |
|
Relative stability of conformers in various solvents (implicit solvent) |
|
Physicochemical and ADMET properties (e.g., pKa, solubility, permeability, logP) |
|
Quantum mechanical optimization structure in implicit solvent including normal modes |
|
Quantum mechanical calculation electrostatic potential in implicit solvent |
|
Parametrization for docking or MD (<50 heavy atoms) |
|
Calculation Quantum mechanical properties (e.g., spectra) |
|
Reactivity calculation using quantum mechanical methods |
| |
| II. |
Proteins in solution (< 1500 AAs) |
|
Analysis/Prediction of 3D structures including reliability analysis and structural comparison |
|
Stability of fold, H-bonds, flexibility of loops |
|
Water/ion site occupancy |
|
Extended NMR ensemble (MD with NOE restraints) |
|
Conformations induced by non-standard residues |
| |
| III. |
Membranes and mebrane proteins (< 1500 AAs) |
|
Simulation of membranes with defined composition |
|
Analysis/Prediction of 3D structures including reliability analysis and structural comparison |
|
Stability of fold, H-bonds, flexibility of loops |
| |
| IV. |
Nucleic Acids (< 40 nucleotides) |
|
Analysis/Prediction of 3D structures including reliability analysis and structural comparison |
|
Stability of fold, H-bonds |
|
Chemical modifications nucleic acids and their modelling |
| |
| V. |
Biomolecular Complexes - Combinations of above plus water/ions (<200.000 atoms) |
|
Predicted 3D from FASTA/PDB and SMILES |
|
Assembly of the complex system |
|
Types of interactions (charged, H-bonds, stacking, water bridge, sigma-hole, covalent) |
|
Occupancy of H-bonds, interaction fingerprints, MM-GBSA interaction energy |
|
Virtual Screening (100 ligans -10 poses - know binding poquet) |
|
QSAR model activity |
|
Virtual Screening (AHL) |
|
Virtual Screening (Large libraries, blind docking) |
|
Binding free energy of ions |
|
Covalent Docking |
|
Restrained md (e.g., Mass-spectroscopy linker ) |