Exploring the free-energy landscapes of biological systems with steered molecular dynamics

AFM Force Spectroscopy and Steered Molecular Dynamics Simulation of Protein Contactin 4

(2016) J. Strzelecki   ACTA PHYSICA POLONICA A

Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations

(2010) L.Y. Chen   BIOPHYSICAL CHEMISTRY

Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies

(2010) Thomas Steinbrecher et al.   CURRENT MEDICINAL CHEMISTRY

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

(2010) Julien Michel et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Determination of equilibrium free energy from nonequilibrium work measurements

(2010) L. Y. Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin

(2010) Camilo Aponte-Santamaría et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Forced unbinding of GPR17 ligands from wild type and R255I mutant receptor models through a computational approach

(2010) Chiara Parravicini et al.   BMC STRUCTURAL BIOLOGY

Methods for Calculating the Entropy and Free Energy and their Application to Problems Involving Protein Flexibility and Ligand Binding

(2009) Hagai Meirovitch et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

(2009) David L. Mobley et al.   Journal of Chemical Theory and Computation

Binding of arachidonic acid and two flavonoid inhibitors to human 12- and 15-lipoxygenases: a steered molecular dynamics study

(2009) Carolina Mascayano et al.   JOURNAL OF MOLECULAR MODELING

Assessment of Nonequilibrium Free Energy Methods

(2009) Benjamin P. Cossins et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Steered Molecular Dynamics Simulations Reveal the Likelier Dissociation Pathway of Imatinib from Its Targeting Kinases c-Kit and Abl

(2009) Li-Jun Yang et al.   PLoS One

Ligand unbinding from the estrogen receptor: A computational study of pathways and ligand specificity

(2009) Sofia Burendahl et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics

(2008) L. Y. Chen   JOURNAL OF CHEMICAL PHYSICS

Protein−Ligand Binding Affinity by Nonequilibrium Free Energy Methods

(2008) Benjamin P. Cossins et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The antigen–antibody unbinding process through steered molecular dynamics of a complex of an Fv fragment and lysozyme

(2008) Itsuo Hanasaki et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Mechanism of selectivity in aquaporins and aquaglyceroporins

(2008) J. S. Hub et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diffusion of Glycerol through Escherichia coli Aquaglyceroporin GlpF

(2007) Jérôme Hénin et al.   BIOPHYSICAL JOURNAL