MC+MD
in-house Monte-Carlo, in-house minimization, rdkit, Vina.
Gasteiger charges for Vina scores
Rdkit was used to generate 1000 conformations from SMILES strings for each ligand.
These conformations were aligned to the most similar template from PDB, using LIGSIFT and the best conformation was
manually adjusted to fit the template. This conformation was used as a starting one for MD and MC.
2000 MC steps
1000 minimization steps
Monte-Carlo refinement was done using in-house MC package. Prealigned
structures were used as starting points. Accepted steps were clustered and cluster centers were retained.
For MD simulations prealigned structures were used as starting points. Results were clustered and cluster
centers were added to cluster centers from MC. The whole mix was minimized using in-house minimization and
scored by Vina (scoring only, no refinement) and LIGSIFT. Non-minimized MD conformations were included in the
mix as well. For each ligand 10 best Vina scores were taken, out of which 5 best LIGSIFT scores were
kept and ranked according to LIGSIFT score.
No
Yes