| experiment |
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| 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.
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| results |
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The results are displayed in two different tables (table 1, table 2). The tables are ordered by PDB code.
First table columns:
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the PDB code |
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the ligand name |
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the number of solutions found |
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the energy and rmsd of the first ranked solution |
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energy, rmsd, and rank of the first solution with an rmsd below 1.0Å |
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energy, rmsd, and rank of the first solution with minimal rmsd |
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run time for the base placement |
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run time for the incremental complex construction |
Second table columns:
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the PDB code |
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the ligand name |
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number of solutions predicted by FlexX |
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energy and rank of the solutions with minimal rmsd |
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energy and rank of the solution with rmsd < 1.0Å |
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energy and rank of the solution with rmsd < 1.5Å |
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energy and rank of the solution with rmsd < 2.0Å |
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energy and rank of the solution with rmsd < 2.5Å |
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run time for base placement |
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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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