QM - Accelrys

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QM/MM Applications: Improving Docking Accuracy • • Pipeline Pilot workflow for CDOCKER-QM-CDOCKER © 2007 Accelrys, Inc. Available options: ESP, Hirshfeld, Mulliken Available Options: Coarse/Medium/Fine. Affects the basis set, k-point, and SCF convergence criteria Available Options: local (LDA) potentials (PWC, VWN) and gradientcorrected (GGA) potentials (PW91, BP, PBE, BLYP, BOP, VWN-BP, RPBE, HCTH). 20
QM/MM Applications: Improving Docking Accuracy • CDOCKER-QM-CDOCKER on AstexDiverse dataset: success by RMSD bin 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% © 2007 Accelrys, Inc. < 0.5 Å < 1.0 Å < 1.5 Å < 2.0 Å Only single, top-ranked pose for each PDB complex considered CDOCKER First Pose QM-CDOCKER First Pose 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% CDOCKER Best Pose QM-CDOCKER Best < 0.5 Å < 1.0 Å < 1.5 Å < 2.0 Å Best-RMSD pose (to X-ray) out of 10 docked poses considered 21
Page 1 and 2: Towards Increased Accuracy in Compu
Page 3 and 4: QM/MM overview • Combine QM and M
Page 5 and 6: QM/MM Overview Anatomy of QM/MM mac
Page 7 and 8: DMol3 DMol Functionals 3 Functional
Page 9 and 10: QUANTUMm Overview • Total energy
Page 11 and 12: QUANTUMm Issue: Broken QM ↔ MM bo
Page 13 and 14: QUANTUMm User Interface • DS QUAN
Page 15 and 16: QM/MM Calculation: Setup in Discove
Page 17 and 18: QM/MM Background: Partial Charge An
Page 19: QM/MM Applications: Improving Docki
Page 23 and 24: QM/MM Application: Optimizing Heme
Page 25 and 26: QM/MM Application: Modeling Metals
Page 27 and 28: QM/MM Application: Optimization of
Page 33 and 34: Thank you!!! • Thank You for atte
Page 35: HOMO/LUMO Visualization (Work in Pr

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