MC-refine
In house Monte-Carlo/LIGSIFT/RDKIT
Gasteiger charges
Starting ligand conformations were prepared by by RDKIT.
3000 MC steps
1000 step minimization (700 receptor fixed, 300 unfixed)
The most similar ligands from PDB database were chosen, and
target ligands were aligned using LIGSIFT and manual alignment of those, whose alignment was failed by LIGSIFT.
The best poses were subsequently refined using our Monte-Carlo protocol, clusterized, minimized and
rescored both by Vina-like energy function and LIGSIFT. Remark: for molecules starting with DMSO- we
used provided DMSO crystal structure.
No
Yes