Computational protocol: Competitive Binding of a Benzimidazole to the Histone-BindingPocket of the Pygo PHD Finger

Similar protocols

Protocol publication

[…] Docking simulations were performed with HADDOCK version 2.1 linked to CNS version 1.3. CNS topology parameters for CF16 were generated using the PRODRG server, and partial charges were assigned from MOPAC semiempirical calculations using the PM7 Hamiltonian. The starting coordinates for PHD–HD1 were taken from 4UP0, with hydrogen atoms added (using PyMol version 1.6). Unambiguous NOE distance restraints were each applied as a symmetric biharmonic potential without penalty in the distance range 1.8–3.8 Å, 1.8–4.6 Å, or 1.8–5.7 Å, according to the intensity of the NOE correlation (note that the tightening of these ranges by 1 Å each resulted in essentially the same models as shown in Figure A). For the final models, 200 structures were refined with explicit water, all of which occupied a single cluster. […]

Pipeline specifications

Software tools HADDOCK, CNS, PRODRG, PyMOL
Applications Drug design, Small-angle scattering, Protein structure analysis
Organisms Dipturus trachyderma
Diseases Neoplasms
Chemicals Benzothiazoles