FlexX performance on 'FlexX-200'

experiment


Redocking 1avd from 200data-set, resulting in an rmsd of
0.8Å. The native structure is shown in red.

In order to extensively test FlexX and prepare it for "real life" docking, FlexX was evaluated using a test set of 200 protein ligand complexes from the PDB. Each ligand was separated from the protein-ligand-complex and hand-fixed concerning protonation, aromaticity, delocalisation, and formal charges.

The prepared ligands were then docked back into the receptor active site using FlexX Release 2 and CORINATM for the generation of ring configurations.

This evaluation was performed on a 20-node cluster running dual AMD Athlon MP 2000+ processors.

results

The results are displayed in two different tables (table 1, table 2). The tables are ordered by PDB code.

First table columns:

  • the PDB code
  • the ligand name
  • the number of solutions found
  • the energy and rmsd of the first ranked solution
  • energy, rmsd, and rank of the first solution with an rmsd below 1.0Å
  • energy, rmsd, and rank of the first solution with minimal rmsd
  • run time for the base placement
  • run time for the incremental complex construction

Second table columns:

  • the PDB code
  • the ligand name
  • number of solutions predicted by FlexX
  • energy and rank of the solutions with minimal rmsd
  • energy and rank of the solution with rmsd < 1.0Å
  • energy and rank of the solution with rmsd < 1.5Å
  • energy and rank of the solution with rmsd < 2.0Å
  • energy and rank of the solution with rmsd < 2.5Å
  • run time for base placement
  • run time for incremental complex construction

For the 200 complexes, FlexX uses on average 18s computing time for the complex construction on a single node.

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