Charles L. Brooks

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

Abstract A first‐generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic har...

CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model

Abstract A fluctuating charge (FQ) force field is applied to molecular dynamics simulations for six small proteins in explicit polarizable solvent represented by the TIP4P‐FQ po...

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecula...

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology

CHARMM: The biomolecular simulation program

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades ...

Deformable stochastic boundaries in molecular dynamics

A new approach to studying localized chemical events in condensed phases is developed. The approach provides a simple and convenient method for reducing the total number of solv...

Improved Treatment of the Protein Backbone in Empirical Force Fields

Empirical force field-based calculations of proteins, including protein-folding studies, have improved our understanding of the relationship of their structure to their biologic...

Stochastic boundary conditions for molecular dynamics simulations of ST2 water