Prediction of the unknown: inspiring experience with the CAPRI experiment

Proteins
Efrat Ben-ZeevMiriam Eisenstein

Abstract

We submitted predictions for all seven targets in the CAPRI experiment. For four targets, our submitted models included acceptable, medium accuracy predictions of the structures of the complexes, and for a fifth target we identified the location of the binding site of one of the molecules. We used a weighted-geometric docking algorithm in which contacts involving specified parts of the surfaces of either one or both molecules were up-weighted or down-weighted. The weights were based on available structural and biochemical data or on sequence analyses. The weighted-geometric docking proved very useful for five targets, improving the complementarity scores and the ranks of the nearly correct solutions, as well as their statistical significance. In addition, the weighted-geometric docking promoted formation of clusters of similar solutions, which include more accurate predictions.

References

Mar 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·E Katchalski-KatzirI A Vakser
Jan 1, 1987·Annual Review of Biochemistry·D C Wiley, J J Skehel
Mar 29, 1996·Journal of Molecular Biology·O LichtargeF E Cohen
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·M Levitt, M Gerstein
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 29, 2000·Proteins·R NajmanovichM Edelman
Oct 25, 2000·Protein Science : a Publication of the Protein Society·C A EarhartD H Ohlendorf
Mar 13, 2001·Journal of Molecular Biology·E ThouveninE Hewat
Oct 26, 2001·Journal of Molecular Biology·K DecanniereL Wyns
Feb 16, 2002·Protein Science : a Publication of the Protein Society·Alexander HeifetzMiriam Eisenstein
Mar 12, 2002·Virology·C Barbey-MartinM Knossow
Apr 19, 2002·The Journal of Biological Chemistry·Aline DesmyterChristian Cambillau
Oct 3, 2002·Proceedings of the National Academy of Sciences of the United States of America·Sonia FieulaineSylvie Nessler

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Citations

Apr 20, 2004·Current Opinion in Structural Biology·Shoshana J Wodak, Raúl Méndez
Feb 17, 2005·Bioinformatics·Carlos J Camacho, Chao Zhang
Mar 14, 2013·PloS One·Rezaul ChowdhuryChandrajit Bajaj
Jul 17, 2004·Comptes rendus biologies·Miriam Eisenstein, Ephraim Katchalski-Katzir

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