Journal
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume 30, Issue 7, Pages 533-539Publisher
SPRINGER
DOI: 10.1007/s10822-016-9920-5
Keywords
Protonation; Tautomerization; Free energy calculation; Thermodynamic integration; Free energy perturbation; Protein-ligand binding affinity
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Funding
- Merck Research Laboratories (MRL) Postdoctoral Research Fellows Program
- Office of Advanced Cyberinfrastructure (OAC)
- Direct For Computer & Info Scie & Enginr [1515572] Funding Source: National Science Foundation
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In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck-Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER TI and Schrodinger FEP+ are shown that should encourage others to explore the value of TI in routine Structure-based Drug Design.
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