Molecular Dynamics Simulations of Acylpeptide Hydrolase Bound to Chlorpyrifosmethyl Oxon and Dichlorvos

Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays

(2014) Huimin Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Free Energy Predictions of Ligand Binding to an α-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations

(2014) Jan K. Marzinek et al.   Journal of Chemical Information and Modeling

Regularized linearization for quantum nonlinear optical cavities: application to degenerate optical parametric oscillators

(2014) Carlos Navarrete-Benlloch et al.   OPTICS EXPRESS

Understanding the folding and stability of a designed WW domain protein with replica exchange molecular dynamics simulations

(2013) Jian-ping Hu et al.   MOLECULAR SIMULATION

Molecular Dynamics Simulations of DNA-Free and DNA-Bound TAL Effectors

(2013) Hua Wan et al.   PLoS One

Alteration of substrate specificities of thermophilic α/β hydrolases through domain swapping and domain interface optimization

(2012) Xiaoli Zhou et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

Evaluation of DOCK 6 as a pose generation and database enrichment tool

(2012) Scott R. Brozell et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal α-helix in an acylaminoacyl peptidase

(2012) Elena Papaleo et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Understanding the molecular basis of MK2–p38α signaling complex assembly: insights into protein–protein interaction by molecular dynamics and free energy studies

(2012) Ying Yang et al.   Molecular BioSystems

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

(2012) Elena Papaleo et al.   PLoS One

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Optimized Potential of Mean Force Calculations for Standard Binding Free Energies

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

Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

(2011) Hironori Kokubo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Multiwfn: A multifunctional wavefunction analyzer

(2011) Tian Lu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding

(2011) Diego E. B. Gomes et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multilevel Parallelization of AutoDock 4.2

(2011) Andrew P Norgan et al.   Journal of Cheminformatics

Structure and Catalysis of Acylaminoacyl Peptidase

(2010) Veronika Harmat et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Docking Validation Resources: Protein Family and Ligand Flexibility Experiments

(2010) Sudipto Mukherjee et al.   Journal of Chemical Information and Modeling

A novel class of protease targets of phosphatidylethanolamine-binding proteins (PEBP): a study of the acylpeptide hydrolase and the PEBP inhibitor from the archaeon Sulfolobus solfataricus

(2010) Gianna Palmieri et al.   Molecular BioSystems

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

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

The conserved N-terminal helix of acylpeptide hydrolase from archaeon Aeropyrum pernix K1 is important for its hyperthermophilic activity

(2008) Zuoming Zhang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Glu88 in the non-catalytic domain of acylpeptide hydrolase plays dual roles: Charge neutralization for enzymatic activity and formation of salt bridge for thermodynamic stability

(2008) Guangyu Yang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Molecular Dynamics Simulations of Hemoglobin A in Different States and Bound to DPG: Effector-Linked Perturbation of Tertiary Conformations and HbA Concerted Dynamics

(2007) Monique Laberge et al.   BIOPHYSICAL JOURNAL