Free energy calculation of single molecular interaction using Jarzynski’s identity method: the case of HIV-1 protease inhibitor system

Cell and molecular biomechanics: perspectives and challenges

(2013) Baohua Ji et al.   ACTA MECHANICA SOLIDA SINICA

Optimized Potential of Mean Force Calculations for Standard Binding Free Energies

(2011) Ignasi Buch et al.   Journal of Chemical Theory and Computation

Strength of Hydrogen Bond Network Takes Crucial Roles in the Dissociation Process of Inhibitors from the HIV-1 Protease Binding Pocket

(2011) Dechang Li et al.   PLoS One

Structure-based design of carbon nanotubes as HIV-1 protease inhibitors: Atomistic and coarse-grained simulations

(2010) Yuan Cheng et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics

(2010) Justin A. Lemkul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors

(2010) Francesco Colizzi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors

(2009) Dechang Li et al.   JOURNAL OF CHEMICAL PHYSICS

Nanomechanical properties of vimentin intermediate filament dimers

(2009) Zhao Qin et al.   NANOTECHNOLOGY

COARSE GRAINED MODELING OF BIOPOLYMERS AND PROTEINS: METHODS AND APPLICATIONS

(2009) DECHANG LI et al.   International Journal of Applied Mechanics

Recent Advances in Optical Tweezers

(2008) Jeffrey R. Moffitt et al.   Annual Review of Biochemistry

Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex

(2008) Michel A. Cuendet et al.   BIOPHYSICAL JOURNAL

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation

Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors

(2007) Kitiyaporn Wittayanarakul et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY