The Citing articles tool gives a list of articles citing the current article. The citing articles come from EDP Sciences database, as well as other publishers participating in CrossRef Cited-by Linking Program. You can set up your personal account to receive an email alert each time this article is cited by a new article (see the menu on the right-hand side of the abstract page).
Employing nano-SnFe2O4 in the synthesis of arylbenzimidazoles, the computational study of the reaction mechanism, and examining the products as putative human transmembrane protein activators
Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set
Marina P. Oliveira, Yan M. H. Gonçalves, S. Kashef Ol Gheta, et al. Journal of Chemical Theory and Computation 18(11) 6757 (2022) https://doi.org/10.1021/acs.jctc.2c00524
Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition
Darren Demapan, Jörg Kussmann, Christian Ochsenfeld and Qiang Cui Journal of Chemical Theory and Computation 18(4) 2530 (2022) https://doi.org/10.1021/acs.jctc.1c00714
Reverse Protonation of Buried Ion-Pairs in Staphylococcal Nuclease Mutants
Reaction-field electrostatics in molecular dynamics simulations: development of a conservative scheme compatible with an atomic cutoff
Alžbeta Kubincová, Sereina Riniker and Philippe H. Hünenberger Physical Chemistry Chemical Physics 22(45) 26419 (2020) https://doi.org/10.1039/D0CP03835K
Multi-level free energy simulation with a staged transformation approach
Molecular dynamics study of taxadiene synthase catalysis
Andrés M. Escorcia, Jeaphianne P. M. van Rijn, Gui‐Juan Cheng, Patrick Schrepfer, Thomas B. Brück and Walter Thiel Journal of Computational Chemistry 39(19) 1215 (2018) https://doi.org/10.1002/jcc.25184
Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods
Anders S. Christensen, Jimmy C. Kromann, Jan H. Jensen and Qiang Cui The Journal of Chemical Physics 147(16) (2017) https://doi.org/10.1063/1.4985605
Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin
An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy
Fang Bai, Sha Liao, Junfeng Gu, et al. Journal of Chemical Information and Modeling 55(4) 833 (2015) https://doi.org/10.1021/ci500647f
Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization
Charging Free Energy Calculations Using the Generalized Solvent Boundary Potential (GSBP) and Periodic Boundary Condition: A Comparative Analysis Using Ion Solvation and Oxidation Free Energy in Proteins
Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions
Computational design of protein–ligand binding: Modifying the specificity of asparaginyl‐tRNA synthetase
Anne Lopes, Marcel Schmidt Am Busch and Thomas Simonson Journal of Computational Chemistry 31(6) 1273 (2010) https://doi.org/10.1002/jcc.21414
Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl‐transferase P‐site using molecular dynamics simulations with restraining potentials
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
Microscopic pKa Analysis of Glu286 in Cytochrome c Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model
B. R. Brooks, C. L. Brooks, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, et al. Journal of Computational Chemistry 30(10) 1545 (2009) https://doi.org/10.1002/jcc.21287
QM/MM Study of the Monomeric Red Fluorescent Protein DsRed.M1
Elsa Sanchez-Garcia, Markus Doerr, Ya-Wen Hsiao and Walter Thiel The Journal of Physical Chemistry B 113(52) 16622 (2009) https://doi.org/10.1021/jp9069042
Tetracycline-Tet Repressor Binding Specificity: Insights from Experiments and Simulations
Christophe Chipot, Alan E. Mark, Vijay S. Pande and Thomas Simonson Springer Series in CHEMICAL PHYSICS, Free Energy Calculations 86 463 (2007) https://doi.org/10.1007/978-3-540-38448-9_13
Ammonium Scanning in an Enzyme Active Site
Damien Thompson, Christine Lazennec, Pierre Plateau and Thomas Simonson Journal of Biological Chemistry 282(42) 30856 (2007) https://doi.org/10.1074/jbc.M704788200
The tetracycline: Mg2+ complex: A molecular mechanics force field
Molecular Dynamics Simulations Show That Bound Mg2+ Contributes to Amino Acid and Aminoacyl Adenylate Binding Specificity in Aspartyl-tRNA Synthetase through Long Range Electrostatic Interactions
The use of a generalized born model for the analysis of protein conformational transitions: A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY)
Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues
G. Archontis, K. A. Watson, Q. Xie, G. Andreou, E. D. Chrysina, S. E. Zographos, N. G. Oikonomakos and M. Karplus Proteins: Structure, Function, and Bioinformatics 61(4) 984 (2005) https://doi.org/10.1002/prot.20641
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
An improved method for nonbonded list generation: Rapid determination of near‐neighbor pairs
Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks and Martin Karplus Journal of Computational Chemistry 24(2) 222 (2003) https://doi.org/10.1002/jcc.10123
Product-assisted catalysis in base-excision DNA repair
J. Christopher Fromme, Steven D. Bruner, Wei Yang, Martin Karplus and Gregory L. Verdine Nature Structural & Molecular Biology 10(3) 204 (2003) https://doi.org/10.1038/nsb902
The missing link between thermodynamics and structure in F
1
-ATPase
Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase11Edited by A. R. Fersht
Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht
Georgios Archontis, Thomas Simonson, Dino Moras and Martin Karplus Journal of Molecular Biology 275(5) 823 (1998) https://doi.org/10.1006/jmbi.1997.1470
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
A. D. MacKerell, D. Bashford, M. Bellott, et al. The Journal of Physical Chemistry B 102(18) 3586 (1998) https://doi.org/10.1021/jp973084f
Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium-loaded states