Multiscale simulation of molecular processes in cellular environments

Hydrodynamic effects on β-amyloid (16-22) peptide aggregation

(2016) Mara Chiricotto et al.   JOURNAL OF CHEMICAL PHYSICS

Evaluation of the coarse-grained OPEP force field for protein-protein docking

(2016) Philipp Kynast et al.   BMC Biophysics

Technical advances in molecular simulation since the 1980s

(2015) Martin J. Field   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Force-Sensitive Autoinhibition of the von Willebrand Factor Is Mediated by Interdomain Interactions

(2015) Camilo Aponte-Santamaría et al.   BIOPHYSICAL JOURNAL

Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies

(2015) Jessica Nasica-Labouze et al.   CHEMICAL REVIEWS

Inhibition of protein aggregation and amyloid formation by small molecules

(2015) Andrew J Doig et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Open boundary molecular dynamics

(2015) R. Delgado-Buscalioni et al.   European Physical Journal-Special Topics

Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics

(2015) Fabio Sterpone et al.   Journal of Chemical Theory and Computation

Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field

(2015) Maria Kalimeri et al.   JOURNAL OF NON-CRYSTALLINE SOLIDS

The physical basis of protein misfolding disorders

(2015) Tuomas P. J. Knowles et al.   PHYSICS TODAY

Hydrodynamic collective effects of active protein machines in solution and lipid bilayers

(2015) Alexander S. Mikhailov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

(2014) Fabio Sterpone et al.   CHEMICAL SOCIETY REVIEWS

Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction

(2014) Yimin Shen et al.   Journal of Chemical Theory and Computation

Effects of Macromolecular Crowding on Amyloid Beta (16–22) Aggregation Using Coarse-Grained Simulations

(2014) David C. Latshaw et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulations of Protein Aggregation: Insights from Atomistic and Coarse-Grained Models

(2014) Alex Morriss-Andrews et al.   Journal of Physical Chemistry Letters

On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation

(2013) Tadashi Ando et al.   BIOPHYSICAL JOURNAL

Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation

(2013) Fabio Sterpone et al.   Journal of Chemical Theory and Computation

PRIMO: A Transferable Coarse-Grained Force Field for Proteins

(2013) Parimal Kar et al.   Journal of Chemical Theory and Computation

Anomalous transport in the crowded world of biological cells

(2013) Felix Höfling et al.   REPORTS ON PROGRESS IN PHYSICS

Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk

(2012) Leonardo Darré et al.   Journal of Chemical Theory and Computation

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Advances in multi-domain lattice Boltzmann grid refinement

(2012) D. Lagrava et al.   JOURNAL OF COMPUTATIONAL PHYSICS

The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins

(2012) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing

(2012) Aram Davtyan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assessing the Quality of the OPEP Coarse-Grained Force Field

(2011) Alessandro Barducci et al.   Journal of Chemical Theory and Computation

Protein self-diffusion in crowded solutions

(2011) F. Roosen-Runge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unfolding the A2 Domain of Von Willebrand Factor with the Optical Trap

(2010) Junyi Ying et al.   BIOPHYSICAL JOURNAL

Elongational Flow Induces the Unfolding of von Willebrand Factor at Physiological Flow Rates

(2010) Charles E. Sing et al.   BIOPHYSICAL JOURNAL

Macromolecular dynamics in crowded environments

(2010) Carlos Echeverria et al.   JOURNAL OF CHEMICAL PHYSICS

Effects of Proteins on Protein Diffusion

(2010) Yaqiang Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations

(2009) M. Bernaschi et al.   COMPUTER PHYSICS COMMUNICATIONS

Effect of β-sheet propensity on peptide aggregation

(2009) Giovanni Bellesia et al.   JOURNAL OF CHEMICAL PHYSICS

Structural specializations of A2, a force-sensing domain in the ultralarge vascular protein von Willebrand factor

(2009) Q. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Catch Bonds in Adhesion

(2008) Wendy Thomas   Annual Review of Biomedical Engineering

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

Crowding Effects on Diffusion in Solutions and Cells

(2008) James A. Dix et al.   Annual Review of Biophysics

Multiscale Simulation of Nanobiological Flows

(2008) Maria Fyta et al.   COMPUTING IN SCIENCE & ENGINEERING

Self-Assembly of the β2-Microglobulin NHVTLSQ Peptide Using a Coarse-Grained Protein Model Reveals a β-Barrel Species

(2008) Wei Song et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

(2007) Matej Praprotnik et al.   Annual Review of Physical Chemistry