SDA 7: A modular and parallel implementation of the simulation of diffusional association software

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

(2014) Paolo Mereghetti et al.   BMC Biophysics

Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose Iβ

(2013) Emal M. Alekozai et al.   CELLULOSE

Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions

(2012) Paolo Mereghetti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Biomolecular electrostatics and solvation: a computational perspective

(2012) Pengyu Ren et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Finding a Needle in a Haystack: The Role of Electrostatics in Target Lipid Recognition by PH Domains

(2012) Craig N. Lumb et al.   PLoS Computational Biology

Characterization of the Ligand Receptor Encounter Complex and Its Potential for in Silico Kinetics-Based Drug Development

(2011) Karim M. ElSawy et al.   Journal of Chemical Theory and Computation

On the structure and dynamics of the complex of the nucleosome and the linker histone

(2011) Georgi V. Pachov et al.   NUCLEIC ACIDS RESEARCH

Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

(2010) Paolo Mereghetti et al.   BIOPHYSICAL JOURNAL

Browndye: A software package for Brownian dynamics

(2010) Gary A. Huber et al.   COMPUTER PHYSICS COMMUNICATIONS

ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent

(2010) Daria B. Kokh et al.   Journal of Chemical Theory and Computation

The Impact of Viral RNA on the Association Rates of Capsid Protein Assembly: Bacteriophage MS2 as a Case Study

(2010) Karim M. ElSawy et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Association of Cytochrome c with Membrane-Bound Cytochrome c Oxidase Proceeds Parallel to the Membrane Rather Than in Bulk Solution

(2009) Alexander Spaar et al.   BIOPHYSICAL JOURNAL

Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions

(2009) Uwe Winter et al.   JOURNAL OF CHEMICAL PHYSICS

On the Contributions of Diffusion and Thermal Activation to Electron Transfer betweenPhormidium laminosumPlastocyanin and Cytochromef: Brownian Dynamics Simulations with Explicit Modeling of Nonpolar Desolvation Interactions and Electron Transfer Events

(2009) Razif R. Gabdoulline et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water

(2008) F. Iori et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein-protein docking by simulating the process of association subject to biochemical constraints

(2008) Domantas Motiejunas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS