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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
Cited by
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011) · Current Computer Aided-Drug Design · doi:10.2174/157340911795677602 · Cited by 3,771
Parallel tempering: Theory, applications, and new perspectives
Earl, D. J., & Deem, M. W. (2005) · Physical Chemistry Chemical Physics · doi:10.1039/b509983h · Cited by 1,313
Knowledge-based scoring function to predict protein-ligand interactions
Gohlke, H., Hendlich, M., & Klebe, G. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3371 · Cited by 1,157
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
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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- CoChat. (2026). Citation check: SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence. https://app.cochat.ai/papers/10.1021/ja960751u
- The paper
- DeWitte, R. S., & Shakhnovich, E. I. (1996). SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence. Journal of the American Chemical Society. https://doi.org/10.1021/ja960751u
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
