Manuel Rueda
Manuel Rueda
Computational Biologist
Verified email at scripps.edu
Title
Cited by
Cited by
Year
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment
I Kufareva, M Rueda, V Katritch, G Dock, RC Stevens, R Abagyan
Structure 19 (8), 1108-1126, 2011
3052011
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
M Michino, E Abola, CL Brooks, JS Dixon, J Moult, RC Stevens
Nature Reviews Drug Discovery 8 (6), 455-463, 2009
2822009
A consensus view of protein dynamics
M Rueda, C Ferrer-Costa, T Meyer, A Pérez, J Camps, JL Gelpí, M Orozco
Proceedings of the National Academy of Sciences 104 (3), 796-801, 2007
2432007
Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution Part 1. Cytosine
SA Trygubenko, TV Bogdan, M Rueda, M Orozco, FJ Luque, J Šponer, ...
Physical Chemistry Chemical Physics 4 (17), 4192-4203, 2002
1912002
Thorough validation of protein normal mode analysis: a comparative study with essential dynamics
M Rueda, P Chacón, M Orozco
Structure 15 (5), 565-575, 2007
1622007
Recipes for the selection of experimental protein conformations for virtual screening
M Rueda, G Bottegoni, R Abagyan
Journal of chemical information and modeling 50 (1), 186-193, 2010
1442010
Whole-genome sequencing of a healthy aging cohort
GA Erikson, DL Bodian, M Rueda, B Molparia, ER Scott, ...
Cell 165 (4), 1002-1011, 2016
1432016
GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex
V Katritch, M Rueda, PCH Lam, M Yeager, R Abagyan
Proteins: Structure, Function, and Bioinformatics 78 (1), 197-211, 2010
1292010
The structure and dynamics of DNA in the gas phase
M Rueda, SG Kalko, FJ Luque, M Orozco
Journal of the American Chemical Society 125 (26), 8007-8014, 2003
1292003
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes
M Rueda, G Bottegoni, R Abagyan
Journal of chemical information and modeling 49 (3), 716-725, 2009
1052009
Essential dynamics: a tool for efficient trajectory compression and management
T Meyer, C Ferrer-Costa, A Pérez, M Rueda, A Bidon-Chanal, FJ Luque, ...
Journal of Chemical Theory and Computation 2 (2), 251-258, 2006
1052006
Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?
M Rueda, E Cubero, CA Laughton, M Orozco
Biophysical Journal 87 (2), 800-811, 2004
962004
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories
T Meyer, M D'Abramo, A Hospital, M Rueda, C Ferrer-Costa, A Pérez, ...
Structure 18 (11), 1399-1409, 2010
952010
FlexServ: an integrated tool for the analysis of protein flexibility
J Camps, O Carrillo, A Emperador, L Orellana, A Hospital, M Rueda, ...
Bioinformatics 25 (13), 1709-1710, 2009
892009
G-quadruplexes can maintain their structure in the gas phase
M Rueda, FJ Luque, M Orozco
Journal of the American Chemical Society 128 (11), 3608-3619, 2006
882006
Systematic exploitation of multiple receptor conformations for virtual ligand screening
G Bottegoni, W Rocchia, M Rueda, R Abagyan, A Cavalli
PloS one 6 (5), e18845, 2011
692011
Exploring the essential dynamics of B-DNA
A Pérez, JR Blas, M Rueda, JM López-Bes, X de la Cruz, M Orozco
Journal of chemical theory and computation 1 (5), 790-800, 2005
622005
Approaching elastic network models to molecular dynamics flexibility
L Orellana, M Rueda, C Ferrer-Costa, JR Lopez-Blanco, P Chacón, ...
Journal of Chemical Theory and Computation 6 (9), 2910-2923, 2010
562010
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics
A Emperador, O Carrillo, M Rueda, M Orozco
Biophysical journal 95 (5), 2127-2138, 2008
552008
ALiBERO: evolving a team of complementary pocket conformations rather than a single leader
M Rueda, M Totrov, R Abagyan
Journal of chemical information and modeling 52 (10), 2705-2714, 2012
452012
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Articles 1–20