Systematic coarse-grained modeling of complexation between small interfering RNA and polycations

Martini Coarse-Grained Force Field: Extension to DNA

(2015) Jaakko J. Uusitalo et al.   Journal of Chemical Theory and Computation

First-in-man Phase 1 Clinical Trial of Gene Therapy for Advanced Pancreatic Cancer: Safety, Biodistribution, and Preliminary Clinical Findings

(2015) Louis Buscail et al.   MOLECULAR THERAPY

Simulation and Experimental Assembly of DNA–Graft Copolymer Micelles with Controlled Morphology

(2015) Zonghui Wei et al.   ACS Biomaterials-Science & Engineering

Simulation and Experimental Assembly of DNA–Graft Copolymer Micelles with Controlled Morphology

(2015) Zonghui Wei et al.   ACS Biomaterials Science & Engineering

A molecular dynamics simulation study on the effect of lipid substitution on polyethylenimine mediated siRNA complexation

(2013) Chongbo Sun et al.   BIOMATERIALS

Rapid parameterization of small molecules using the force field toolkit

(2013) Christopher G. Mayne et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Targeting the Blind Spot of Polycationic Nanocarrier-Based siRNA Delivery

(2012) Mengyao Zheng et al.   ACS Nano

Plasmid-Templated Shape Control of Condensed DNA-Block Copolymer Nanoparticles

(2012) Xuan Jiang et al.   ADVANCED MATERIALS

Role of Generation, Architecture, pH and Ionic Strength on Successful siRNA Delivery and Transfection by Hybrid PPV-PAMAM Dendrimers

(2012) G. M. Pavan et al.   CURRENT MEDICINAL CHEMISTRY

Novel polyethylenimine-derived nanoparticles forin vivogene delivery

(2012) Soma Patnaik et al.   Expert Opinion on Drug Delivery

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

In Vivo Gene Delivery by Nonviral Vectors: Overcoming Hurdles?

(2012) Yuan Zhang et al.   MOLECULAR THERAPY

RNA therapeutics: beyond RNA interference and antisense oligonucleotides

(2012) Ryszard Kole et al.   NATURE REVIEWS DRUG DISCOVERY

Fluorescent Nanorods and Nanospheres for Real-Time In Vivo Probing of Nanoparticle Shape-Dependent Tumor Penetration

(2011) Vikash P. Chauhan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The effect of pH on PAMAM dendrimer–siRNA complexation — Endosomal considerations as determined by molecular dynamics simulation

(2011) Defang Ouyang et al.   BIOPHYSICAL CHEMISTRY

Molecular Dynamics Simulations of DNA/PEI Complexes: Effect of PEI Branching and Protonation State

(2011) Chongbo Sun et al.   BIOPHYSICAL JOURNAL

Polycation-Based Gene Therapy: Current Knowledge and New Perspectives

(2011) Marcio J. Tiera et al.   CURRENT GENE THERAPY

Molecular modeling and in vivo imaging can identify successful flexible triazine dendrimer-based siRNA delivery systems

(2011) Olivia M. Merkel et al.   JOURNAL OF CONTROLLED RELEASE

Poly(amidoamine)-based Dendrimer/siRNA Complexation Studied by Computer Simulations: Effects of pH and Generation on Dendrimer Structure and siRNA Binding

(2011) Kostas Karatasos et al.   MACROMOLECULAR BIOSCIENCE

Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine

(2011) Kirill A Afonin et al.   Nature Protocols

Geometry and surface characteristics of gold nanoparticles influence their biodistribution and uptake by macrophages

(2010) Arnida et al.   EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS

Structure, Dynamics, and Energetics of siRNA−Cationic Vector Complexation: A Molecular Dynamics Study

(2010) Defang Ouyang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Molecular Dynamics Simulations of DNA Condensation by Block Copolymer and Formation of Core−Corona Structures

(2010) Jesse Ziebarth et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Complexation of siRNA with Dendrimer: A Molecular Modeling Approach

(2010) V. Vasumathi et al.   MACROMOLECULES

Effect of chain stiffness on the morphology of polyelectrolyte complexes. A Monte Carlo simulation study

(2010) C.F. Narambuena et al.   POLYMER

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

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

Degradable polyethylenimines as DNA and small interfering RNA carriers

(2009) D Jere et al.   Expert Opinion on Drug Delivery

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Stability of Asymmetric Lipid Bilayers Assessed by Molecular Dynamics Simulations

(2009) Santi Esteban-Martín et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The promises and pitfalls of RNA-interference-based therapeutics

(2009) Daniela Castanotto et al.   NATURE

Extracellular Barriers toin VivoPEI and PEGylated PEI Polyplex-Mediated Gene Delivery to the Liver

(2008) Rob S. Burke et al.   BIOCONJUGATE CHEMISTRY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation