The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Molecular dynamics simulations and drug discovery
Open accessAbstract
This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule ligands can play in drug discovery, including the identification of cryptic or allosteric binding sites, the enhancement of traditional virtual-screening methodologies, and the direct prediction of small-molecule binding energies. The limitations of current simulation methodologies, including the high computational costs and approximations of molecular forces required, are also discussed. With constant improvements in both computer power and algorithm design, the future of computer-aided drug design is promising; molecular dynamics simulations are likely to play an increasingly important role.
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Cites
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
The Amber biomolecular simulation programs
Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535
Implications of protein flexibility for drug discovery
Teague, S. J. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1129 · Cited by 755
Folding funnels, binding funnels, and protein function
Tsai, C., Kumar, S., Ma, B., & Nussinov, R. (1999) · Protein Science · doi:10.1110/ps.8.6.1181 · Cited by 648
Folding funnels and binding mechanisms
Ma, B., Kumar, S., Tsai, C.-J., & Nussinov, R. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.9.713 · Cited by 594
Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations
Ma, B., Shatsky, M., Wolfson, H. J., & Nussinov, R. (2002) · Protein Science · doi:10.1110/ps.21302 · Cited by 420
Folding funnels and conformational transitions via hinge-bending motions
Kumar, S., Ma, B., Tsai, C.-J., Wolfson, H., & Nussinov, R. (1999) · Cell Biochemistry and Biophysics · doi:10.1007/bf02738169 · Cited by 94
Cited by
Wang, L., Wu, Y., Deng, Y., Kim, B., Pierce, L., Krilov, G., Lupyan, D., Robinson, S., Dahlgren, M. K., Greenwood, J., et al. (2015) · Journal of the American Chemical Society · doi:10.1021/ja512751q · Cited by 1,313
Enhanced sampling techniques in molecular dynamics simulations of biological systems
Bernardi, R. C., Melo, M. C. R., & Schulten, K. (2015) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.10.019 · Cited by 757
A Review on Applications of Computational Methods in Drug Screening and Design
Lin, X., Li, X., & Lin, X. (2020) · Molecules · doi:10.3390/molecules25061375 · Cited by 718
The future of molecular dynamics simulations in drug discovery
Borhani, D. W., & Shaw, D. E. (2012) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-011-9517-y · Cited by 313
“MD simulations seem to be good at identifying low-energy protein conformations that harbor cryptic drug binding sites [27].”
BackgroundComputational chemistry for water-splitting electrocatalysis
Miao, L., Jia, W., Cao, X., & Jiao, L. (2024) · Chemical Society Reviews · doi:10.1039/d2cs01068b · Cited by 241
Metadata
- Authors
- Durrant, J. D., & McCammon, J. A.
- Venue
- BMC Biology
- Published
- 2011-10-28
- Volume
- 9
- Issue
- 1
- Pages
- 71-71
- ISSN
- 1741-7007 (ISSN-L)
- OpenAlex
- W2118571345
- Cited by
- 1,403
- References
- 7
- FWCI
- 40.07
- Type
- journal article
- Language
- en
- Open access
- gold
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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.
