Molecular Dynamics Simulations of Human Beta-Defensin Type 3 Crossing Different Lipid Bilayers

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

(2019) Giray Enkavi et al.   CHEMICAL REVIEWS

Translocation of Human β Defensin Type 3 through a Neutrally Charged Lipid Membrane: A Free Energy Study

(2018) Rabeta Yeasmin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Different dynamics and pathway of disulfide bonds reduction of two human defensins, a molecular dynamics simulation study

(2017) Liqun Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure and dynamics of Penetratin’s association and translocation to a lipid bilayer

(2017) Ignacio J. General et al.   AIP Advances

Mechanisms and consequences of bacterial resistance to antimicrobial peptides

(2016) D.I. Andersson et al.   DRUG RESISTANCE UPDATES

Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers

(2016) W. F. Drew Bennett et al.   Journal of Chemical Theory and Computation

Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor

(2016) George Hedger et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

(2016) Sun Young Woo et al.   Scientific Reports

Lipid-II Independent Antimicrobial Mechanism of Nisin Depends On Its Crowding And Degree Of Oligomerization

(2016) Ashutosh Prince et al.   Scientific Reports

Membrane disruptive antimicrobial activities of human β-defensin-3 analogs

(2015) U.S. Sudheendra et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

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

Human β-defensin 3 contains an oncolytic motif that binds PI(4,5)P2 to mediate tumour cell permeabilisation

(2015) Thanh Kha Phan et al.   Oncotarget

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins

(2013) Ali May et al.   BIOINFORMATICS

Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD

(2013) Toni Giorgino   COMPUTER PHYSICS COMMUNICATIONS

Human β-defensin-3 structure motifs that are important in CXCR4 antagonism

(2013) Zhimin Feng et al.   FEBS Journal

Engineering Antimicrobial Peptides with Improved Antimicrobial and Hemolytic Activities

(2013) Jun Zhao et al.   Journal of Chemical Information and Modeling

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

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

Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations

(2012) James Gumbart et al.   BIOPHYSICAL JOURNAL

Membrane damage and repair in primary monocytes exposed to human β-defensin-3

(2012) Anthony B. Lioi et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Parallel Generalized Born Implicit Solvent Calculations with NAMD

(2011) David E. Tanner et al.   Journal of Chemical Theory and Computation

The Membrane-Bound Structure and Topology of a Human α-Defensin Indicate a Dimer Pore Mechanism for Membrane Disruption

(2010) Yuan Zhang et al.   BIOCHEMISTRY

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology

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

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions

(2009) Andrzej J. Rzepiela et al.   FARADAY DISCUSSIONS

Toroidal pores formed by antimicrobial peptides show significant disorder

(2008) Durba Sengupta et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Linear Analogues of Human β-Defensin 3: Concepts for Design of Antimicrobial Peptides with Reduced Cytotoxicity to Mammalian Cells

(2008) Shouping Liu et al.   CHEMBIOCHEM

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

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

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