0nqfo-LigandScoringProtocol.txt

Name

AlGDock

Software

OpenEye QUACPAC
modeller 9.18
UCSF dock6
AmberTools 14
NAMD 2.9

Parameters

binding site max radius 6 Å
High temperature 600k
Low temperature 300K
cooling 10 cycles
docking 17 cycles
Each cycle consists of 1000 iterations of Hamiltonian Monte Carlo
NAMD OBC solvent model

Method

In AlGDock based on Implicit Ligand Theory(Minh, 2012), receptor only need to calculate once, and only ligands need simulation. It’s basically made up by two parts, cooling and docking. In both processes, only the ligand molecule is flexible. With cooling, the temperature of the system (only ligand) is progressively changed from 600k to 300k. With docking, receptor-ligand interactions are models by interpolating a precomputed 3D grid. The process consists of reducing the temperature and scaling the strength of the interaction grid from 0 to 1.During sampling, the ligands were treated as desolvated type.

Answer 1

No