docking program flexx  (Tripos Inc)

Journal: Communications chemistry

Article Title: Decrypting a Cryptic Allosteric Pocket in H. pylori Glutamate Racemase

doi: 10.1038/s42004-021-00605-z

Figure Lengend Snippet: The graph is divided into two phases, depicted on the left and the right, respectively. On the left half of the chart, we describe the selection of the best receptor and docking protocol combination; snapshots from MD simulations of ~ 800 ns were clustered and centroids were examined for their ROC performance (ability to discriminate between decoys and known hits). The best performing pair was “2JFZclstr3” as the receptor (derived from the PDB structure 2JFZ, as described in the Methods section) and docking was performed with FlexX (BiosolveIT), as described in the Methods section. The flowchart on the right-hand side is the actual virtual screening protocol that employs the validated 2JFZclstr3-FlexX (receptor and docking protocol) pair, including the experimental biophysical hit validation using SPR. The screening library employed was AnalytiCon’s MEGx natural products library.

Article Snippet: Two different docking programs where then used since each takes a different approach for ligand placement and for searching minimum energy confirmations: FlexX (part of LeadIT available from BioSolveIT GmbH) 51 – 52 and MOE 2016 38 .

Techniques: Selection, Derivative Assay, Biomarker Discovery