Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations

Revealing the activation mechanism of autoinhibited RalF by integrated simulation and experimental approaches

(2021) Balint Dudas et al.   Scientific Reports

New Structural insights into Kir channel gating from molecular simulations, HDX-MS and functional studies

(2020) Charline Fagnen et al.   Scientific Reports

Scalable molecular dynamics on CPU and GPU architectures with NAMD

(2020) James C. Phillips et al.   JOURNAL OF CHEMICAL PHYSICS

Nucleotide-Specific Autoinhibition of Full-Length K-Ras4B Identified by Extensive Conformational Sampling

(2020) Balint Dudas et al.   Frontiers in Molecular Biosciences

The allosteric activation mechanism of a phospholipase A2-like toxin from Bothrops jararacussu venom: a dynamic description

(2020) Antoniel A. S. Gomes et al.   Scientific Reports

Conformational selection dominates binding of steroids to human cytochrome P450 17A1

(2019) F. Peter Guengerich et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanistic Insights into the Effect of Ligands on Structural Stability and Selectivity of Sulfotransferase 2A1 (SULT2A1)

(2019) Jingxuan Zhu et al.   ACS Omega

Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners

(2018) Martin Šrejber et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Structural Dynamics of DPP-4 and Its Influence on the Projection of Bioactive Ligands

(2018) Simone Pantaleão et al.   MOLECULES

Insights into molecular mechanisms of drug metabolism dysfunction of human CYP2C9*30

(2018) Maxime Louet et al.   PLoS One

The NSAID allosteric site of human cytosolic sulfotransferases

(2017) Ting Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The structure of the catechin-binding site of human sulfotransferase 1A1

(2016) Ian Cook et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sulfotransferase 1A1 Substrate Selectivity: A Molecular Clamp Mechanism

(2015) Ian Cook et al.   BIOCHEMISTRY

Integrated structure- and ligand-basedin silicoapproach to predict inhibition of cytochrome P450 2D6

(2015) Virginie Y. Martiny et al.   BIOINFORMATICS

The impact of molecular dynamics on drug design: applications for the characterization of ligand–macromolecule complexes

(2015) Jérémie Mortier et al.   DRUG DISCOVERY TODAY

Structural plasticity in the human cytosolic sulfotransferase dimer and its role in substrate selectivity and catalysis

(2015) Zachary E. Tibbs et al.   Drug Metabolism and Pharmacokinetics

Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis

(2015) Gautier Moroy et al.   Future Medicinal Chemistry

In SilicoPrediction of Human Sulfotransferase 1E1 Activity Guided by Pharmacophores from Molecular Dynamics Simulations

(2015) Christin Rakers et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Exploring Free Energy Landscapes of Large Conformational Changes: Molecular Dynamics with Excited Normal Modes

(2015) Mauricio G. S. Costa et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Sulfotransferase genetic variation: from cancer risk to treatment response

(2013) Jaclyn Daniels et al.   DRUG METABOLISM REVIEWS

Sulfonation of Maternal Steroids is a Conserved Metabolic Pathway in Vertebrates

(2013) R. T. Paitz et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

High Accuracyin SilicoSulfotransferase Models

(2013) Ian Cook et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Advances in Molecular Modeling of Human Cytochrome P450 Polymorphism

(2013) Virginie Y. Martiny et al.   JOURNAL OF MOLECULAR BIOLOGY

In Silico Mechanistic Profiling to Probe Small Molecule Binding to Sulfotransferases

(2013) Virginie Y. Martiny et al.   PLoS One

A Nucleotide-Gated Molecular Pore Selects Sulfotransferase Substrates

(2012) Ian Cook et al.   BIOCHEMISTRY

The Gate That Governs Sulfotransferase Selectivity

(2012) Ian Cook et al.   BIOCHEMISTRY

Reactions and enzymes in the metabolism of drugs and other xenobiotics

(2012) Bernard Testa et al.   DRUG DISCOVERY TODAY

Crystal structures of human sulfotransferases: insights into the mechanisms of action and substrate selectivity

(2012) Dong Dong et al.   Expert Opinion on Drug Metabolism & Toxicology

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

Structure-based Drug Metabolism Predictions for Drug Design

(2009) Hao Sun et al.   Chemical Biology & Drug Design

Dimerization Is Responsible for the Structural Stability of Human Sulfotransferase 1A1

(2009) L.-Y. Lu et al.   DRUG METABOLISM AND DISPOSITION

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Sulfotransferases, sulfatases and formylglycine-generating enzymes: a sulfation fascination

(2008) Pavla Bojarová et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

(2008) H. Lee Woodcock et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY