Rueda M - Search Results

1

Systematic exploitation of multiple receptor conformations for virtual ligand screening.

Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A. Bottegoni G, et al. Among authors: rueda m. PLoS One. 2011;6(5):e18845. doi: 10.1371/journal.pone.0018845. Epub 2011 May 17. PLoS One. 2011. PMID: 21625529 Free PMC article.

2

Ligand-guided receptor optimization.

Katritch V, Rueda M, Abagyan R. Katritch V, et al. Among authors: rueda m. Methods Mol Biol. 2012;857:189-205. doi: 10.1007/978-1-61779-588-6_8. Methods Mol Biol. 2012. PMID: 22323222

3

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes.

Rueda M, Bottegoni G, Abagyan R. Rueda M, et al. J Chem Inf Model. 2009 Mar;49(3):716-25. doi: 10.1021/ci8003732. J Chem Inf Model. 2009. PMID: 19434904 Free PMC article.

4

Recipes for the selection of experimental protein conformations for virtual screening.

Rueda M, Bottegoni G, Abagyan R. Rueda M, et al. J Chem Inf Model. 2010 Jan;50(1):186-93. doi: 10.1021/ci9003943. J Chem Inf Model. 2010. PMID: 20000587 Free PMC article.

5

ALiBERO: evolving a team of complementary pocket conformations rather than a single leader.

Rueda M, Totrov M, Abagyan R. Rueda M, et al. J Chem Inf Model. 2012 Oct 22;52(10):2705-14. doi: 10.1021/ci3001088. Epub 2012 Sep 17. J Chem Inf Model. 2012. PMID: 22947092 Free PMC article.

6

GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex.

Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R. Katritch V, et al. Among authors: rueda m. Proteins. 2010 Jan;78(1):197-211. doi: 10.1002/prot.22507. Proteins. 2010. PMID: 20063437 Free PMC article.

7

SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.

Rueda M, Katritch V, Raush E, Abagyan R. Rueda M, et al. Bioinformatics. 2010 Nov 1;26(21):2784-5. doi: 10.1093/bioinformatics/btq504. Epub 2010 Sep 24. Bioinformatics. 2010. PMID: 20871105 Free PMC article.

8

Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters.

Pallara C, Rueda M, Abagyan R, Fernández-Recio J. Pallara C, et al. Among authors: rueda m. J Chem Theory Comput. 2016 Jul 12;12(7):3236-49. doi: 10.1021/acs.jctc.6b00204. Epub 2016 Jun 28. J Chem Theory Comput. 2016. PMID: 27294484

9

From Homology Models to a Set of Predictive Binding Pockets-a 5-HT_1A Receptor Case Study.

Warszycki D, Rueda M, Mordalski S, Kristiansen K, Satała G, Rataj K, Chilmonczyk Z, Sylte I, Abagyan R, Bojarski AJ. Warszycki D, et al. Among authors: rueda m. J Chem Inf Model. 2017 Feb 27;57(2):311-321. doi: 10.1021/acs.jcim.6b00263. Epub 2017 Jan 18. J Chem Inf Model. 2017. PMID: 28055203 Free PMC article.

10

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment.

Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R; GPCR Dock 2010 participants. Kufareva I, et al. Among authors: rueda m. Structure. 2011 Aug 10;19(8):1108-26. doi: 10.1016/j.str.2011.05.012. Structure. 2011. PMID: 21827947 Free PMC article.

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