Accurate binding mode prediction:
CovDock is built upon a foundation of the time-tested Glide docking algorithm and Prime structure refinement methodology for accurate prediction of non-covalently docked poses. Glide quickly samples a large pool of initial poses for the pre-reactive species and Prime simultaneously optimizes the ligand pose and attachment residue to produce a sound physical chemistry. The resultant accuracy outperforms other docking programs in achieving lower RMS deviations from native co-crystallized structures.
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Complete workflow:
CovDock performs a series of automated steps based on a simple setup from the Maestro graphical interface or from the command line. First, CovDock docks the pre-reactive ligand to determine viable poses that bring the reactive group into close proximity with the reactive receptor residue. Then the covalent bond is formed for the top scoring complex structures, the covalently attached ligand is sampled, and the complexes are scored using all-atom molecular mechanics with the OPLS force field and VSGB2.0 implicit solvent model.
Intuitive graphical interface:
Schrödinger’s intuitive graphical user interface, Maestro, provides easy-to-use panels for straightforward set-up of experiments, easy visualization, and efficient analysis of CovDock results.
Citations and Acknowledgements
ö Zhu, K.; Borrelli, K.W.; Greenwood, J.R.; Day, T.; Abel, R.; Farid, R.S.; Harder, E., 'Docking covalent inhibitors: A parameter free approach to pose prediction and scoring,' J. Chem. Inf. Model., 2014, 54, 1932−1940
CDock2_0.9.8.zip
2 Security-lock slot Lock the dock to a desk, table, or other fixture through a compatible security cable lock. 3 Audio connector Connect a headphone or a headset with a 3.5-mm (0.14-inch) and 4-pole plug. 4 10 USB 3.1 connector Gen 2 Connect a USB-compatible device to.
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15 pin HD D-Sub (HD-15), 25 pin D-Sub (DB-25), 4 pin USB Type A, 50 pin D-Sub (DB-50), 6 pin mini-DIN (PS/2 style), 9 pin D-Sub (DB-9), IrDA, RJ-45, mini-phone mono 3.5 mm, mini-phone stereo 3.5 mm. Download the latest release of cDock; 2. Open the downloaded dmg file; 3. Allow cDock to move itself to the Applications folder; 5. Disable System Integrity Protection; 6. CDock will need to install or update it’s System Components; 7. If you are on 10.13 or below you may re-enable System Integrity Protection; 8.