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Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
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- Journal of Molecular Recognition, 2010, v. 23, n. 2, p. 128, doi. 10.1002/jmr.996
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- Article
Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement.
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- Nature, 2005, v. 436, n. 7052, p. 852, doi. 10.1038/nature03888
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- Article
Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola.
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- Nature Communications, 2016, v. 7, n. 9, p. 12753, doi. 10.1038/ncomms12753
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- Article
Mechanism of potassium ion uptake by the Na<sup>+</sup>/K<sup>+</sup>-ATPase.
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- Nature Communications, 2015, v. 6, n. 7, p. 7622, doi. 10.1038/ncomms8622
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- Article
Activation pathway of Src kinase reveals intermediate states as targets for drug design.
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- Nature Communications, 2014, v. 5, n. 3, p. 3397, doi. 10.1038/ncomms4397
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- Article
Ion channels and ion selectivity.
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- Essays in Biochemistry, 2017, v. 61, n. 2, p. 201, doi. 10.1042/EBC20160074
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- Article
Theoretical and computational models of biological ion channels.
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- Quarterly Reviews of Biophysics, 2004, v. 37, n. 1, p. 15, doi. 10.1017/S0033583504003968
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- Article
G Protein-Coupled Receptors: What a Difference a 'Partner' Makes.
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- International Journal of Molecular Sciences, 2014, v. 15, n. 1, p. 1112, doi. 10.3390/ijms15011112
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- Article
Dominant solvation effects from the primary shell of hydration: Approximation for molecular dynamics simulations.
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- Biopolymers, 1995, v. 35, n. 2, p. 171, doi. 10.1002/bip.360350205
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- Article
Structural basis for the coupling between activation and inactivation gates in K<sup>+</sup> channels.
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- Nature, 2010, v. 466, n. 7303, p. 272, doi. 10.1038/nature09136
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- Article
Architecture and assembly of the Gram-positive cell wall.
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- Molecular Microbiology, 2013, v. 88, n. 4, p. 664, doi. 10.1111/mmi.12203
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- Article
Computational study of the W260A activating mutant of Src tyrosine kinase.
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- Protein Science: A Publication of the Protein Society, 2016, v. 25, n. 1, p. 219, doi. 10.1002/pro.2731
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- Article
Structure and electrostatic property of cytoplasmic domain of ZntB transporter.
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- Protein Science: A Publication of the Protein Society, 2009, v. 18, n. 10, p. 2043, doi. 10.1002/pro.215
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- Article
Bulletin de la Société Paul Claudel. 2023 - 2, n° 240 - Deux Annonce faite à Marie: un opéra et un film restauré.
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- 2023
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- Book Review
Conformational dynamics of ligand-dependent alternating access in LeuT.
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- Nature Structural & Molecular Biology, 2014, v. 21, n. 5, p. 472, doi. 10.1038/nsmb.2816
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- Article
Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain.
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- Nature Structural & Molecular Biology, 2014, v. 21, n. 3, p. 244, doi. 10.1038/nsmb.2768
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- Article
Protonation of key acidic residues is critical for the K<sup>+</sup>-selectivity of the Na/K pump.
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- Nature Structural & Molecular Biology, 2011, v. 18, n. 10, p. 1159, doi. 10.1038/nsmb.2113
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- Article
The hidden energetics of ligand binding and activation in a glutamate receptor.
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- Nature Structural & Molecular Biology, 2011, v. 18, n. 3, p. 283, doi. 10.1038/nsmb.2010
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- Article
On the structural basis of modal gating behavior in K<sup>+</sup> channels.
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- Nature Structural & Molecular Biology, 2011, v. 18, n. 1, p. 67, doi. 10.1038/nsmb.1968
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- Article
Molecular driving forces determining potassium channel slow inactivation.
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- Nature Structural & Molecular Biology, 2007, v. 14, n. 11, p. 1062, doi. 10.1038/nsmb1309
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- Article
Molecular determinants of gating at the potassium-channel selectivity filter.
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- Nature Structural & Molecular Biology, 2006, v. 13, n. 4, p. 311, doi. 10.1038/nsmb1069
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- Article
Les nouvelles idoles du primitivisme: une mythologie des modernes.
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- Svet Literatury: Casopis Pro Novodobé Literatury, 2022, p. 102, doi. 10.14712/23366729.2022.3.7
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- Article
Les nouvelles idoles du primitivisme: une mythologie des modernes.
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- Svet Literatury: Casopis Pro Novodobé Literatury, 2022, n. 66, p. 102, doi. 10.14712/23366729.2022.3.7
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- Article
Atomic mutagenesis in ion channels with engineered stoichiometry.
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- eLife, 2016, p. 1, doi. 10.7554/eLife.18976
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- Article
The selectivity of the Na<sup>+</sup>/K<sup>+</sup>-pump is controlled by binding site protonation and self-correcting occlusion.
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- eLife, 2016, p. 1, doi. 10.7554/eLife.16616
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- Article
Shifts in the selectivity filter dynamics cause modal gating in K<sup>+</sup> channels.
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- Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-018-07973-6
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- Article
The emergence of protein dynamics simulations: how computational statistical mechanics met biochemistry.
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- European Physical Journal H, 2022, v. 47, n. 1, p. 1, doi. 10.1140/epjh/s13129-022-00043-y
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- Article
The breakthrough of a quantum chemist by classical dynamics: Martin Karplus and the birth of computer simulations of chemical reactions.
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- European Physical Journal H, 2021, v. 46, n. 1, p. 1, doi. 10.1140/epjh/s13129-021-00013-w
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- Article
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.
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- Nature Protocols, 2022, v. 17, n. 4, p. 1114, doi. 10.1038/s41596-021-00676-1
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- Article
Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.
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- PLoS Computational Biology, 2015, v. 11, n. 10, p. 1, doi. 10.1371/journal.pcbi.1004368
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- Article
Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model.
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- PLoS Computational Biology, 2014, v. 10, n. 4, p. 1, doi. 10.1371/journal.pcbi.1003521
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- Article
<i>Escherichia coli</i> Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations.
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- PLoS Computational Biology, 2014, v. 10, n. 2, p. 1, doi. 10.1371/journal.pcbi.1003475
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- Article
Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms.
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- PLoS Computational Biology, 2008, v. 4, n. 3, p. 1, doi. 10.1371/journal.pcbi.1000047
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- Article
Crystal structure of an archaeal CorB magnesium transporter.
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- Nature Communications, 2021, v. 12, p. 1, doi. 10.1038/s41467-021-24282-7
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- Article
Molecular Mechanisms of K[+] Selectivity in Na/K Pump.
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- Australian Journal of Chemistry, 2012, v. 65, n. 5, p. 8
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- Article
Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols.
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- Journal of Computational Chemistry, 2020, v. 41, n. 5, p. 427, doi. 10.1002/jcc.26064
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- Article
CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations.
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- Journal of Computational Chemistry, 2020, v. 41, n. 5, p. 415, doi. 10.1002/jcc.26032
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- Article
Combining the polarizable Drude force field with a continuum electrostatic Poisson–Boltzmann implicit solvation model.
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- Journal of Computational Chemistry, 2018, v. 39, n. 22, p. 1707, doi. 10.1002/jcc.25345
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- Article
CHARMM-GUI 10 years for biomolecular modeling and simulation.
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- Journal of Computational Chemistry, 2017, v. 38, n. 15, p. 1114, doi. 10.1002/jcc.24660
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- Article
Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.
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- Journal of Computational Chemistry, 2015, v. 36, n. 19, p. 1473, doi. 10.1002/jcc.23937
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- Article
Modeling induction phenomena in amino acid cation-π interactions.
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- Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2018, v. 137, n. 12, p. 1, doi. 10.1007/s00214-018-2376-z
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- Article
Recovery from slow inactivation in K<sup>+</sup> channels is controlled by water molecules.
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- Nature, 2013, v. 501, n. 7465, p. 121, doi. 10.1038/nature12395
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- Article
Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29239-y
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- Article
A distinct mechanism of C-type inactivation in the Kv-like KcsA mutant E71V.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28866-9
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- Article
Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores.
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- Journal of Computational Chemistry, 2012, v. 33, n. 3, p. 331, doi. 10.1002/jcc.21952
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- Article
Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions.
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- Journal of Computational Chemistry, 2010, v. 31, n. 4, p. 811, doi. 10.1002/jcc.21369
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- Article
Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects.
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- Journal of Computational Chemistry, 2007, v. 28, n. 10, p. 1634, doi. 10.1002/jcc.20652
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- Article
Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13C14 and C15N16 bonds in the retinal of bacteriorhodopsin.
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- Journal of Computational Chemistry, 1999, v. 20, n. 15, p. 1644, doi. 10.1002/(SICI)1096-987X(19991130)20:15<1644::AID-JCC5>3.0.CO;2-Y
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- Article
Mixing quantum-classical molecular dynamics methods applied to intramolecular proton transfer in acetylacetone.
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- Journal of Computational Chemistry, 1997, v. 18, n. 14, p. 1760, doi. 10.1002/(SICI)1096-987X(19971115)18:14<1760::AID-JCC5>3.0.CO;2-I
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- Article
A potential function for computer simulation studies of proton transfer in acetylacetone.
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- Journal of Computational Chemistry, 1997, v. 18, n. 3, p. 368, doi. 10.1002/(SICI)1096-987X(199702)18:3<368::AID-JCC7>3.0.CO;2-S
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- Article