Samuel Genheden
TitleCited byYear
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
S Genheden, U Ryde
Expert opinion on drug discovery 10 (5), 449-461, 2015
6782015
Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3
C Diehl, O Engström, T Delaine, M Håkansson, S Genheden, K Modig, ...
Journal of the American Chemical Society 132 (41), 14577-14589, 2010
1712010
How to obtain statistically converged MM/GBSA results
S Genheden, U Ryde
Journal of computational chemistry 31 (4), 837-846, 2010
1492010
An MM/3D-RISM approach for ligand binding affinities
S Genheden, T Luchko, S Gusarov, A Kovalenko, U Ryde
The Journal of Physical Chemistry B 114 (25), 8505-8516, 2010
1082010
The carbohydrate-binding site in galectin-3 is preorganized to recognize a sugarlike framework of oxygens: ultra-high-resolution structures and water dynamics
K Saraboji, M Håkansson, S Genheden, C Diehl, J Qvist, U Weininger, ...
Biochemistry 51 (1), 296-306, 2011
972011
Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3
C Diehl, S Genheden, K Modig, U Ryde, M Akke
Journal of biomolecular NMR 45 (1-2), 157-169, 2009
732009
Will molecular dynamics simulations of proteins ever reach equilibrium?
S Genheden, U Ryde
Physical Chemistry Chemical Physics 14 (24), 8662-8677, 2012
712012
The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant
S Genheden, O Kuhn, P Mikulskis, D Hoffmann, U Ryde
Journal of chemical information and modeling 52 (8), 2079-2088, 2012
642012
Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies
P Mikulskis, D Cioloboc, M Andrejić, S Khare, J Brorsson, S Genheden, ...
Journal of Computer-Aided Molecular Design, 1-26, 2014
632014
Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA
S Genheden, I Nilsson, U Ryde
Journal of chemical information and modeling 51 (4), 947-958, 2011
582011
Comparison of end‐point continuum‐solvation methods for the calculation of protein–ligand binding free energies
S Genheden, U Ryde
Proteins: Structure, Function, and Bioinformatics 80 (5), 1326-1342, 2012
532012
Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration
S Genheden, P Mikulskis, LH Hu, J Kongsted, P Söderhjelm, U Ryde
Journal of the American Chemical Society 133 (33), 13081-13092, 2011
522011
A large-scale test of free-energy simulation estimates of protein–ligand binding affinities
P Mikulskis, S Genheden, U Ryde
Journal of chemical information and modeling 54 (10), 2794-2806, 2014
502014
Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations
F Godschalk, S Genheden, P Söderhjelm, U Ryde
Physical Chemistry Chemical Physics 15 (20), 7731-7739, 2013
462013
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations
S Genheden, U Ryde
Journal of computational chemistry 32 (2), 187-195, 2011
452011
Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods
P Mikulskis, S Genheden, P Rydberg, L Sandberg, L Olsen, U Ryde
Journal of computer-aided molecular design 26 (5), 527-541, 2012
432012
Comparison of the efficiency of the LIE and MM/GBSA methods to calculate ligand-binding energies
S Genheden, U Ryde
Journal of chemical theory and computation 7 (11), 3768-3778, 2011
422011
Starting-condition dependence of order parameters derived from molecular dynamics simulations
S Genheden, C Diehl, M Akke, U Ryde
Journal of chemical theory and computation 6 (7), 2176-2190, 2010
372010
Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge
S Genheden, AIC Martinez, MP Criddle, JW Essex
Journal of computer-aided molecular design 28 (3), 187-200, 2014
322014
A QM/MM study of the binding of RAPTA ligands to cathepsin B
A Ciancetta, S Genheden, U Ryde
Journal of computer-aided molecular design 25 (8), 729-742, 2011
312011
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Articles 1–20