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Interaction of Phthalates with Lipid Bilayer Membranes
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Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins
Olivier Bignucolo, Christophe Chipot, Stephan Kellenberger and Benoît Roux The Journal of Physical Chemistry B 126(36) 6868 (2022) https://doi.org/10.1021/acs.jpcb.2c04593
A distinct mechanism of C-type inactivation in the Kv-like KcsA mutant E71V
String Method for Protein–Protein Binding Free-Energy Calculations
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Influence of the Treatment of Nonbonded Interactions on the Thermodynamic and Transport Properties of Pure Liquids Calculated Using the 2016H66 Force Field
Yan M. H. Gonçalves, Caroline Senac, Patrick F. J. Fuchs, Philippe H. Hünenberger and Bruno A. C. Horta Journal of Chemical Theory and Computation 15(3) 1806 (2019) https://doi.org/10.1021/acs.jctc.8b00425
Electrostatic interactions in soft particle systems: mesoscale simulations of ionic liquids
Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation
Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization
Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods
Ming Huang, Timothy J. Giese, Tai-Sung Lee and Darrin M. York Journal of Chemical Theory and Computation 10(4) 1538 (2014) https://doi.org/10.1021/ct401013s
Classical Electrostatics for Biomolecular Simulations
G. Andrés Cisneros, Mikko Karttunen, Pengyu Ren and Celeste Sagui Chemical Reviews 114(1) 779 (2014) https://doi.org/10.1021/cr300461d
Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation
Rolf E. Isele-Holder, Wayne Mitchell, Jeff R. Hammond, Axel Kohlmeyer and Ahmed E. Ismail Journal of Chemical Theory and Computation 9(12) 5412 (2013) https://doi.org/10.1021/ct4004614
Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations
Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions
Maria M. Reif, Vincent Kräutler, Mika A. Kastenholz, Xavier Daura and Philippe H. Hünenberger The Journal of Physical Chemistry B 113(10) 3112 (2009) https://doi.org/10.1021/jp807421a
Biophysical Techniques in Photosynthesis
William W. Parson and Arieh Warshel Advances in Photosynthesis and Respiration, Biophysical Techniques in Photosynthesis 26 401 (2008) https://doi.org/10.1007/978-1-4020-8250-4_20
Computational Modeling of Membrane Bilayers
Mikko Karttunen, Jörg Rottler, Ilpo Vattulainen and Celeste Sagui Current Topics in Membranes, Computational Modeling of Membrane Bilayers 60 49 (2008) https://doi.org/10.1016/S1063-5823(08)00002-1
The optimal P3M algorithm for computing electrostatic energies in periodic systems
Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations
Celeste Sagui, Lee G. Pedersen and Thomas A. Darden The Journal of Chemical Physics 120(1) 73 (2004) https://doi.org/10.1063/1.1630791
Long range interactions on wires: A reciprocal space based formalism
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A new reciprocal space based treatment of long range interactions on surfaces
Peter Mináry, Mark E. Tuckerman, Katianna A. Pihakari and Glenn J. Martyna The Journal of Chemical Physics 116(13) 5351 (2002) https://doi.org/10.1063/1.1453397
Computational Methods for Macromolecules: Challenges and Applications
Mark E. Tuckerman, Peter Minary, Katianna Pihakari and Glenn J. Martyna Lecture Notes in Computational Science and Engineering, Computational Methods for Macromolecules: Challenges and Applications 24 381 (2002) https://doi.org/10.1007/978-3-642-56080-4_16
FROM FOLDING THEORIES TO FOLDING PROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding
Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions
Molecular Dynamics - From Classical to Quantum Methods
Fredrik Hedman and Aatto Laaksonen Theoretical and Computational Chemistry, Molecular Dynamics - From Classical to Quantum Methods 7 231 (1999) https://doi.org/10.1016/S1380-7323(99)80040-5
New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations