The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Efficient docking of peptides to proteins without prior knowledge of the binding site
Open accessAbstract
Reliability in docking of ligand molecules to proteins or other targets is an important challenge for molecular modeling. Applications of the docking technique include not only prediction of the binding mode of novel drugs, but also other problems like the study of protein‐protein interactions. Here we present a study on the reliability of the results obtained with the popular AutoDock program. We have performed systematical studies to test the ability of AutoDock to reproduce eight different protein/ligand complexes for which the structure was known, without prior knowledge of the binding site. More specifically, we look at factors influencing the accuracy of the final structure, such as the number of torsional degrees of freedom in the ligand. We conclude that the Autodock program package is able to select the correct complexes based on the energy without prior knowledge of the binding site. We named this application blind docking, as the docking algorithm is not able to “see” the binding site but can still find it. The success of blind docking represents an important finding in the era of structural genomics.
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VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Crystal Structure of Human Cyclophilin A Bound to the Amino-Terminal Domain of HIV-1 Capsid
Gamble, T. R., Vajdos, F. F., Yoo, S., Worthylake, D. K., Houseweart, M., Sundquist, W. I., & Hill, C. P. (1996) · Cell · doi:10.1016/s0092-8674(00)81823-1 · Cited by 706 · cited 1×
“The latter finding hints at the possibility of a combination of blind docking with fragment docking ( Friedman et al. 1994 ) and to studies of proteinprotein interactions.”
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Cited by
Mechanism of Blebbistatin Inhibition of Myosin II
Kovács, M., Tóth, J., Hetényi, C., Málnási-Csizmadia, A., & Sellers, J. R. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m405319200 · Cited by 1,019
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Craddock, T. J. A., St. George, M., Freedman, H., Barakat, K. H., Damaraju, S., Hameroff, S., & Tuszynski, J. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037251 · Cited by 84
Stabilizers of the Max Homodimer Identified in Virtual Ligand Screening Inhibit Myc Function
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Assessing protein homology models with docking reproducibility
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Metadata
- Authors
- Hetényi, C., & van der Spoel, D.
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2002-07
- Volume
- 11
- Issue
- 7
- Pages
- 1729-1737
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- OpenAlex
- W2136513242
- Cited by
- 450
- References
- 2
- FWCI
- 11.00
- Type
- journal article
- Language
- en
- Open access
- bronze
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