The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
HexServer: an FFT-based protein docking server powered by graphics processors
Open accessAbstract
HexServer (http://hexserver.loria.fr/) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes approximately 15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein structures in PDB format to be uploaded, and it produces a ranked list of up to 1000 docking predictions. Knowledge of one or both protein binding sites may be used to focus and shorten the calculation when such information is available. The first 20 predictions may be accessed individually, and a single file of all predicted orientations may be downloaded as a compressed multi-model PDB file. The server is publicly available and does not require any registration or identification by the user.
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Cites
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187
PatchDock and SymmDock: servers for rigid and symmetric docking
Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki481 · Cited by 3,018
ZDOCK: An initial‐stage protein‐docking algorithm
Chen, R., Li, L., & Weng, Z. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10389 · Cited by 1,393 · cited 14×
“In order to illustrate the speed-up given by our GPU-accelerated approach over a conventional Cartesian grid-based FFT docking calculation, we docked the PDB structures given on the HexServer ‘Examples’ page (porcine trypsin and soybean trypsin inhibitor, PDB code 1AVX) using Hex 6.0, HexServer (which invokes Hex 6.0)…”
MethodInfluentialKatchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A. A., Aflalo, C., & Vakser, I. A. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.6.2195 · Cited by 1,107
ClusPro: a fully automated algorithm for protein-protein docking
Comeau, S. R., Gatchell, D. W., Vajda, S., & Camacho, C. J. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh354 · Cited by 824
GRAMM-X public web server for protein-protein docking
Tovchigrechko, A., & Vakser, I. A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl206 · Cited by 807
Efficient Unbound Docking of Rigid Molecules
Duhovny, D., Nussinov, R., & Wolfson, H. J. (2002) · Lecture Notes in Computer Science · doi:10.1007/3-540-45784-4_14 · Cited by 711
The RosettaDock server for local protein-protein docking
Lyskov, S., & Gray, J. J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn216 · Cited by 592
Protein docking using spherical polar Fourier correlations
Ritchie, D. W., & Kemp, G. J. L. (2000) · Proteins: Structure, Function, and Genetics · doi:10.1002/(sici)1097-0134(20000501)39:2<178::aid-prot8>3.0.co;2-6 · Cited by 563
Self-citationAssessment of blind predictions of protein–protein interactions: Current status of docking methods
Méndez, R., Leplae, R., De Maria, L., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10393 · Cited by 418
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Metadata
- Authors
- Macindoe, G., Mavridis, L., Venkatraman, V., Devignes, M.-D., & Ritchie, D. W.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-05-05
- Volume
- 38
- Issue
- Web Server
- Pages
- W445-W449
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2106210646
- Cited by
- 668
- References
- 12
- FWCI
- 8.74
- Type
- journal article
- Language
- en
- Open access
- gold
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