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SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence
Abstract
In this paper, we present SMoG ( S mall Mo lecule G rowth), a novel, straightforward method for de novo lead design and the evidence for its effectiveness. It is based on a simple model for ligand-protein interactions and a scoring that is directly related to the free energy through a knowledge-based potential. A large number of structures are examined by an efficient metropolis Monte Carlo molecular growth algorithm that generates molecules through the adjoining of functional groups directly in the binding region. Thus SMoG is a method that is able to rank a large number of potential compounds according to binding free energy in a short time. In this sense, SMoG represents a step toward an ideal computational tool for ligand design.
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Citations
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Earl, D. J., & Deem, M. W. (2005) · Physical Chemistry Chemical Physics · doi:10.1039/b509983h · Cited by 1,313
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Walters, W. P., Stahl, M. T., & Murcko, M. A. (1998) · Drug Discovery Today · doi:10.1016/s1359-6446(97)01163-x · Cited by 991
The Process of Structure-Based Drug Design
Anderson, A. C. (2003) · Chemistry & Biology · doi:10.1016/j.chembiol.2003.09.002 · Cited by 939
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The maximal affinity of ligands
Kuntz, I. D., Chen, K., Sharp, K. A., & Kollman, P. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.9997 · Cited by 849
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Grinter, S., & Zou, X. (2014) · Molecules · doi:10.3390/molecules190710150 · Cited by 260
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Metadata
- Authors
- DeWitte, R. S., & Shakhnovich, E. I.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 1996-01-01
- Volume
- 118
- Issue
- 47
- Pages
- 11733-11744
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W1965207004
- Cited by
- 262
- References
- 0
- FWCI
- 9.79
- Type
- journal article
- Language
- en
- Open access
- closed
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