8-6-2024

This directory contains the primary results for Surflex-Dock, Vina, and Gnina for the following paper:

Title:     Structure-Based Pose Prediction: Non-Cognate Docking Extended to Macrocyclic Ligands
Authors:   Ann E. Cleves, Himani Tandon, Ajay N. Jain*
Journal:   Journal of Computer-Aided Molecular Design
Submitted: August 2024

Scripts for Surflex-Dock are in SFDock-Scripts (the same were used for both benchmark sets). Scripts for AutoDock Vina are in Vina-Scripts, and scripts for Gnina are in Gnina-scripts.

Each of the PINC and Macro subdirectories contain results for a single target, including the protein and ligand files in
mol2 format. The following is an explanation of the files for PINC/cdk2 (with the other folders being analogous):

      KnownPoses.mol2              # Known poses (either earlier for the temporal set
                                   # or non-macrocycles for the Macro set)
      Test-random.mol2             # Randomized starting conformations for each test ligand
      TestRefClean.mol2            # Reference bound conformations, one per ligand
      protein-01.mol2              # Protein variant 1
         ...
      protein-05.mol2              # Protein variant 5
      ligand-01.mol2               # Cognate ligand of protein variant 1
         ...
      ligand-05.mol2               # Cognate ligand of protein variant 5

      sfdock-rmsquant01            # Results for Surflex-Dock top 1 pose family
      sfdock-rmsquant01-best.mol2  # Best pose for top 1 pose family for each test ligand
      sfdock-rmsquant01-gold.mol2  # Corresponding reference poses
                                   # Analogous files for top 2, 5, and 10 pose families

      vinafam001                   # Analogous results for Vina top 1 pose family
      vinafam001-best.mol2
      vinafam001-gold.mol2
                                   # Analogous files for Vina top 2, 5, 10, and 100 pose families

      gninafam001                  # Analogous files for Gnina top 1, 2, 5, 10, and 100 pose families
      gninafam001-best.mol2
      gninafam001-gold.mol2

