The second type is referred to docking with multiple receptor structures, using pre-generated receptor conformers (Knegtel et al. 1997).
Rather than docking many compound models into a single NMR or crystal structure, each potential ligand is docked into multiple protein conformations, typically extracted from a molecular dynamics simulation.
Notably, we have shown, for the first time, that resveratrol binds directly to multiple docking sites of the extracellular portion of EGFR, thus explaining the rapid dephosphorylation of EGFR on Tyr-1068, with consequent downregulation of AKT signaling.
Because its cognate epitope is repeated on PrP, POM2 can dock to PrP through multiple interactions, yielding extremely high avidities in the femtomolar range [18].
I/O saturation was most apparent at the end of the initial wave of docking jobs when multiple log files are simultaneously written to disk and grid maps for the next docking jobs are loaded.
Hence, to improve runtime efficiency and reduce I/O file operations, we modified the AutoDock 4.0 source code to load the energy grid files only once, while docking multiple ligands in a single run.
The master node distributes the docking jobs to worker nodes, and a worker node executes distributed docking jobs with multiple GPUs by CUDA and all CPU cores by OpenMP thread parallelization.
Current docking algorithms do not allow multiple-ligand simultaneous docking to target protein.
We present the water model parameterization carried out on a set of benchmark complexes and show some preliminary results for docking multiple ligands concurrently.
With the ability of Surflex-Dock to start the docking process with a single or multiple placed fragments, this scoring function can be applied in fragment based drug discovery to optimize attachments onto a pre-placed substructure.
