Molecular insights into substrate binding mechanism of undecaprenyl pyrophosphate with membrane integrated phosphatidyl glycerophosphate phosphatase B (PgpB) using molecular dynamics simulation approach

A Continuum Poisson–Boltzmann Model for Membrane Channel Proteins

(2017) Li Xiao et al.   Journal of Chemical Theory and Computation

Structural Insight into Substrate Selection and Catalysis of Lipid Phosphate Phosphatase PgpB in the Cell Membrane

(2016) Shuilong Tong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Modeling Membrane Protein–Ligand Binding Interactions: The Human Purinergic Platelet Receptor

(2016) D’Artagnan Greene et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson–Boltzmann Equation

(2015) Wesley M. Botello-Smith et al.   Journal of Chemical Information and Modeling

Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase

(2015) Guillaume Manat et al.   PLoS One

Proposed Carrier Lipid-binding Site of Undecaprenyl Pyrophosphate Phosphatase fromEscherichia coli

(2014) Hsin-Yang Chang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal structure of lipid phosphatase Escherichia coli phosphatidylglycerophosphate phosphatase B

(2014) J. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Crystal Structure of MraY, an Essential Membrane Enzyme for Bacterial Cell Wall Synthesis

(2013) B. C. Chung et al.   SCIENCE

Reducing Grid Dependence in Finite-Difference Poisson–Boltzmann Calculations

(2012) Jun Wang et al.   Journal of Chemical Theory and Computation

Dynamical probing of allosteric control in nuclear receptors

(2012) Mark A. Cunningham   JOURNAL OF MOLECULAR MODELING

Cholesterol and POPC segmental order parameters in lipid membranes: solid state1H–13C NMR and MD simulation studies

(2012) Tiago Mendes Ferreira et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods

(2011) Takaharu Mori et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

Simulaid: A simulation facilitator and analysis program

(2010) Mihaly Mezei   JOURNAL OF COMPUTATIONAL CHEMISTRY

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Performance of Nonlinear Finite-Difference Poisson−Boltzmann Solvers

(2009) Qin Cai et al.   Journal of Chemical Theory and Computation

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Achieving energy conservation in Poisson–Boltzmann molecular dynamics: Accuracy and precision with finite-difference algorithms

(2008) Jun Wang et al.   CHEMICAL PHYSICS LETTERS

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

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