Abstract
The 3 ns unrestrained MD simulations were carried out on the DNA/duocarmycin complex based on (1) the classic RESP charge model, and (2) the QM-polarized ligand docking (QPLD)-based charge model. The RMSDs of the trajectories and the ΔGbind of the QPLD model perform much better than the RESP model, with the ΔGbind estimation for QPLD model (-16.11 kcal/mol) versus ΔGbind estimation for RESP model (-10.05 kcal/mol).
Original language | English (US) |
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Pages (from-to) | 542-545 |
Number of pages | 4 |
Journal | Bioorganic and Medicinal Chemistry Letters |
Volume | 18 |
Issue number | 2 |
DOIs | |
State | Published - Jan 15 2008 |
Externally published | Yes |
Keywords
- DNA/duocarmycin complex
- MD simulations
- MM/GBSA
- QM-polarized ligand docking (QPLD)
- RESP charge model
ASJC Scopus subject areas
- Biochemistry
- Molecular Medicine
- Molecular Biology
- Pharmaceutical Science
- Drug Discovery
- Clinical Biochemistry
- Organic Chemistry