Dear All
I have done the docking using CDOCKER and subjected the best pose to "calculate binding energies" . I am confused with the results. Looking forward your kind advice. Thank you
Mai
Summary
| Ligand
Name | Binding Energy
(kcal/mol) | Ligand Energy
(kcal/mol) | Protein Energy
(kcal/mol) | Complex Energy
(kcal/mol) |
|---|
| Y1 | -3.01299 | -5.82643 | -56959.820313 | -56968.65973 | | y2 | 0.00525 | -25.21552 | -57083.328125 | -57108.53840 | | y3 | 1748.23395 | -24.04828 | -57107.84375 | -55383.65808 | | y4 | 1766.36944 | -14.88065 | -57113.234375 | -55361.74558 | | y5 | -14.44135 | -17.46326 | -58234.03125 | -58265.93586 | | y6 | 6.36365 | -33.04279 | -57007.617188 | -57034.29633 | | y8 | 35.03413 | -131.45411 | -57072.492188 | -57168.91217 | | y9 | 38.97631 | -164.69713 | -57072.941406 | -57198.66223 | | y10 | 37.69398 | -230.82655 | -57108.546875 | -57301.67944 | | y11 | 437.42937 | -33.43578 | -57093.972656 | -56689.97907 | | y23 | 0.56362 | -42.75148 | -57229.542969 | -57271.73083 | | y29 | 836.37993 | -20.36960 | -57052.800781 | -56236.79045 | | y30 | -2.08961 | -17.49165 | -57226.328125 | -57245.90939 | | y31 | 23.80605 | -16.16144 | -57264.5 | -57256.85539 | | y32 | -7.66379 | -15.28687 | -58236.800781 | -58259.75144 | | y35 | 60.52812 | -145.34363 | -57174.453125 | -57259.26864 |
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1) How should i interpret the results? by looking for Binding E, or complex E? [the more negative the better it is?]
2) Y2, Y3, Y4, Y6, Y8, Y9, Y10, Y11, Y23, Y29, Y31 and Y35, seems giving me a positive binding energy, which means the compounds are not stable in binding right, but the in vitro assay proved others wise, does that mean there is something wrong in the stimulation (parameters are attached below)?
Parameters
| | Input Receptor | ../Input/3.msv | | Input Ligands | ../Input/3selected_for_bindingE.sd | | Input Group by Property |
| | Flexible Receptor Atom Property | Receptor.Positions, Gold.Protein.RotatedAtoms | | Implicit Solvent Model | Generalized Born with a simple SWitching (GBSW) | | Dielectric Constant | 1 | | Implicit Solvent Dielectric Constant | 80 | | Generalized Born Lambda Constant |
| | Minimum Hydrogen Radius | 1.0 | | Use Non-polar Surface Area | True | | Non-polar Surface Constant | 0.92 | | Non-polar Surface Coefficient | 0.00542 | | Salt Concentration | 0.0 | | Nonbond List Radius | 14.0 | | Nonbond Higher Cutoff Distance | 12.0 | | Nonbond Lower Cutoff Distance | 10.0 | | Electrostatics | Spherical Cutoff | | Kappa | 0.34 | | Order | 4 | | Estimates Entropy | False | | Entropy Temperature | 298.15 | | Parallel Processing | False | | Parallel Processing Batch Size | 25 | | Parallel Processing Server | localhost | | Parallel Processing Server Processes | 2 | | Parallel Processing Preserve Order | True | | Entropy Mode | Translational and Rotational Only | | Entropy Trajectory File |
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