Welcome_to_DockingHome_1308856706244

 

 

Remerciements

 

Ce travail a été financé par la NSF, subvention # 0941318: «CDI Type 1: Combler le fossé entre la prochaine génération d’ordinateurs haute performance hybride basé sur la physique et les modèles de calcul pour la description quantitative de reconnaissance moléculaire», et subvention # 0922657 'MRI: Acquisition d'une installation pour les approches de calcul des problèmes à l'échelle moléculaire», et par l'armée américaine, subvention ARO 54723-CS" L’aide des ordinateurs pour la modélisation de médicaments sur les nouveaux ordinateurs hybrides à haut rendement, et par la bourse # 171595 CONACyT. Les auteurs tiennent à remercier Charles L. Brooks III pour ses précieux conseils et les volontaires de Docking @ Home pour nous fournir des ressources essentielles.

 

 

Références

 

 

[1] D. P. Anderson. Boinc: A system for public-resource

computing and storage. In Proceedings of the 5th

IEEE/ACM International Workshop on Grid Computing.,

pages 4–10, November 2004.

[2] K. Bckbro, S. Lwgren, K. Osterlund, J. Atepo, T. Unge,

J. Hultn, N.M. Bonham, W. Schaal, A. Karln, and

A. Hallberg. Unexpected binding mode of a cyclic

sulfamide hiv-1 protease inhibitor. Journal of Medical

Chemistry, 40:898–902, 1997.

[3] G. Bouvier, N. Evrard-Todeschi, J. P. Girault, and

G. Bertho. Automatic clustering of docking poses in virtual

screening process using self-organising map. Bioinformatics

Advance Access, 2009.

[4] R. L. Cannon, J. V. Dave, and J. C. Bezdek. Efficient

implementation of the fuzzy c-means clustering algorithms.

IEEE Transactions on Pattern Analysis and Machine

Intelligence, 8:248–255, 1986.

[5] S. Ceri and R. Manthey. Chimera: A model and language

for active dood systems. In In Proceedings of the 2nd

East-West Database Workshop, Workshops in Computing,

pages 3–16. Springer, 1994.

[6] M. W. Chang, R. K. Belew, K. S. Carroll, A. J. Olson, and

D. S. Goodsell. Empirical entropic contributions in

computational docking: Evaluation in aps reductase

complexes. Journal of Computational Chemistry,

29:1753–1761, 2008.

[7] F. Dullweber, M.T. Stubbs, D. Musil, J. Strzebecher, and

G. Klebe. Factorising ligand affinity: a combined

thermodynamic and crystallographic study of trypsin and

thrombin inhibition. Journal of Molecular Biology,

313:593–614, 2001.

[8] M. Feig, A. Onufriev, M. S. Lee, W. Im, D. A. Case, and

C. L. Brooks III. Performance comparison of generalized

born and poisson methods in the calculation of electrostatic

solvation energies for protein structures. Journal of

Computational Chemistry, 25:265–84, 2004.

[9] P. C. D. Hawkins, G. L. Warren, A. G. Skillman, and

A. Nicholls. How to do an evaluation: pitfalls and traps. J.

of Computer Aided Molecular Design, 22:179–190, 2008.

[10] W. Humphrey, A. Dalke, and K. Schulten. VMD – Visual

Molecular Dynamics. Journal of Molecular Graphics,

14:33–38, 1996.

[11] A. N. Jain. Bias, reporting, and sharing: computational

evaluations of docking methods. Journal of Computer

Aided Molecular Design, 22:201–212, 2008.

[12] M. S. Lee, M. Feig, F. R. Salsbury Jr., and C. L. Brooks

III. New analytic approximation to the standard molecular

volume definition and its application to generalized born

calculations. Journal of Computational Chemistry,

24:1348–56, 2003.

[13] S. Liang, G. Wang, and Y. Zhou. Refining near-native

protein-protein docking decoys by local resampling and

energy minimization. PROTEINS: Structure, Function,

and Bioinformatics, pages 309–316, 2008.

[14] S. Lorenzen and Y. Zhang. Identification of near-native

structures by clustering protein docking conformations.

PROTEINS: Structure, Function, and Bioinformatics,

68:187–194, 2007.

[15] LPDB - protein-ligand database. http://lpdb.scripps.edu/.

[16] Y. Shen, I. C. Paschalidis, P. Vakili, and S. Vajda. Protein

docking by the underestimation of free energy funnels in

the space of encounter complexes. PLOS Computational

Biology, 4, 2008.

[17] W. S. Student Gosset. The probable error of a mean.

Biometrika, 6:1–25, 1908.

[18] Z. Wang, B.J. Canagarajah, J.C. Boehm, S. Kassis, M.H

Cobb, P.R Young, S. Abdel-Meguid, J.L Adams, and E.J.

Goldsmith. Structural basis of inhibitor selectivity in map

kinases. Structure, 6:1117–28, 1998.

[19] B. L. Welch. The generalization of ’student’s’ problem.

Biometrika, 34:28–35, 1947. 

 

 

Traduction

Alliance Francophone

(Ryzen, Ousermaatre, Bcoz)