Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization

Atomic-Scale Molecular Dynamics Simulations of DNA–Polycation Complexes: Two Distinct Binding Patterns

(2016) Diana A. Kondinskaia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PEP-FOLD3: fasterde novostructure prediction for linear peptides in solution and in complex

(2016) Alexis Lamiable et al.   NUCLEIC ACIDS RESEARCH

The structure and intermolecular forces of DNA condensates

(2016) Jejoong Yoo et al.   NUCLEIC ACIDS RESEARCH

Characterization of the AXH domain of Ataxin-1 using enhanced sampling and functional mode analysis

(2016) Marco A. Deriu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics

(2015) Gül H. Zerze et al.   Journal of Chemical Theory and Computation

Micelle-like Nanoparticles as Carriers for DNA and siRNA

(2015) Gemma Navarro et al.   MOLECULAR PHARMACEUTICS

ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations: Table 2.

(2015) Andrea Pérez-Villa et al.   NUCLEIC ACIDS RESEARCH

Conformational fluctuations of the AXH monomer of Ataxin-1

(2015) Gianvito Grasso et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

(2014) Juyong Lee et al.   Journal of Chemical Theory and Computation

DNA Recognition Process of the Lactose Repressor Protein Studied via Metadynamics and Umbrella Sampling Simulations

(2014) Simone Furini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanistic insight into ligand binding to G-quadruplex DNA

(2014) Francesco Saverio Di Leva et al.   NUCLEIC ACIDS RESEARCH

Investigation of the Josephin Domain Protein-Protein Interaction by Molecular Dynamics

(2014) Marco A. Deriu et al.   PLoS One

A Comparison of DNA Compaction by Arginine and Lysine Peptides: A Physical Basis for Arginine Rich Protamines

(2013) Jason DeRouchey et al.   BIOCHEMISTRY

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

(2013) Christina Bergonzo et al.   Journal of Chemical Theory and Computation

Shaping cancer nanomedicine: the effect of particle shape on the in vivo journey of nanoparticles

(2013) Randall Toy et al.   Nanomedicine

Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study

(2013) Andrea Coletta et al.   NUCLEIC ACIDS RESEARCH

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

(2013) D. Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting the Blind Spot of Polycationic Nanocarrier-Based siRNA Delivery

(2012) Mengyao Zheng et al.   ACS Nano

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

Molecular Dynamics Simulations for Complexation of DNA with 2 kDa PEI Reveal Profound Effect of PEI Architecture on Complexation

(2012) Chongbo Sun et al.   JOURNAL OF PHYSICAL CHEMISTRY B

In Vivo Gene Delivery by Nonviral Vectors: Overcoming Hurdles?

(2012) Yuan Zhang et al.   MOLECULAR THERAPY

Systematic Validation of Protein Force Fields against Experimental Data

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

Understanding the Effect of Polylysine Architecture on DNA Binding Using Molecular Dynamics Simulations

(2011) Robert M. Elder et al.   BIOMACROMOLECULES

Cell transcytosing poly-arginine coated magnetic nanovector for safe and effective siRNA delivery

(2011) Omid Veiseh et al.   BIOMATERIALS

The Binding Process of a Nonspecific Enzyme with DNA

(2011) Chuanying Chen et al.   BIOPHYSICAL JOURNAL

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

(2011) Chongbo Sun et al.   BIOPHYSICAL JOURNAL

Protein–dendron conjugates for DNA binding: understanding the effect of the protein core on multivalency

(2011) Giovanni M. Pavan et al.   RSC Advances

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Computational Insights into the Interactions between DNA and siRNA with “Rigid” and “Flexible” Triazine Dendrimers

(2010) Giovanni M. Pavan et al.   BIOMACROMOLECULES

Thermodynamics of Polyethylenimine-DNA Binding and DNA Condensation

(2010) Kuniharu Utsuno et al.   BIOPHYSICAL JOURNAL

A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets

(2010) Goutam Mukherjee et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Salt bridges: Geometrically specific, designable interactions

(2010) Jason E. Donald et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Understanding the Protonation Behavior of Linear Polyethylenimine in Solutions through Monte Carlo Simulations

(2009) Jesse D. Ziebarth et al.   BIOMACROMOLECULES

Molecular Dynamics Simulations of DNA-Polycation Complex Formation

(2009) Jesse Ziebarth et al.   BIOPHYSICAL JOURNAL

Optimal temperature ladders in replica exchange simulations

(2009) Robert Denschlag et al.   CHEMICAL PHYSICS LETTERS

Efficiency of exchange schemes in replica exchange

(2009) Martin Lingenheil et al.   CHEMICAL PHYSICS LETTERS

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Degradable polyethylenimines as DNA and small interfering RNA carriers

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

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics

(2009) M. Bonomi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Modeling the Multivalent Recognition between Dendritic Molecules and DNA: Understanding How Ligand “Sacrifice” and Screening Can Enhance Binding

(2009) Giovanni M. Pavan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Knocking down barriers: advances in siRNA delivery

(2009) Kathryn A. Whitehead et al.   NATURE REVIEWS DRUG DISCOVERY

Dendrons/dendrimers: quantized, nano-element like building blocks for soft-soft and soft-hard nano-compound synthesis

(2009) Donald A. Tomalia   Soft Matter

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

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

Formulation and Delivery of siRNA by Oleic Acid and Stearic Acid Modified Polyethylenimine

(2008) Aws Alshamsan et al.   MOLECULAR PHARMACEUTICS

Dissociation of minor groove binders from DNA: insights from metadynamics simulations

(2008) A. V. Vargiu et al.   NUCLEIC ACIDS RESEARCH

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS