List of works - Charles L Brooks

A rapid solvent accessible surface area estimator for coarse grained molecular simulations

scientific article

Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units

scientific article published on 24 December 2019

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

scientific article published on October 2009

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins ⬇️

scientific article published on November 1, 2003

An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins

scholarly article

Application of solid-state NMR restraint potentials in membrane protein modeling

scientific article published on 18 April 2008

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

scientific article

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

scientific article

Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations

scientific article published in March 2015

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

scientific article

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

scientific article published on 11 May 2017

Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

scientific article published on 29 April 2013

Constant-pH molecular dynamics using continuous titration coordinates

scientific article published on 01 September 2004

Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions

scientific article published on 9 February 2007

De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein

scientific article published in March 2004

De novo prediction of the structures of M. tuberculosis membrane proteins

scientific article published on 2 April 2008

Evolution and physics in comparative protein structure modeling.

scientific article

Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models

scientific article published on 7 March 2017

Exploring atomistic details of pH-dependent peptide folding

scholarly article

Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network

scientific article published on 21 February 2007

Force Field Influence on the Observation of π-Helical Protein Structures in Molecular Dynamics Simulations

article

Generalized born model with a simple smoothing function

scientific article published in November 2003

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling

scientific article

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

scientific article

Implicit solvation based on generalized Born theory in different dielectric environments

scientific article published in January 2004

Improved model building and assessment of the Calcium-sensing receptor transmembrane domain

scientific article published in April 2008

Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations

scientific article

Linking folding with aggregation in Alzheimer's beta-amyloid peptides

scholarly article

Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations

scientific article published on 3 November 2006

Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation

scientific article published in July 2004

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

scientific article published in August 2003

New analytic approximation to the standard molecular volume definition and its application to generalized born calculations

Novel generalized Born methods

PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements

scientific article published on 4 July 2014

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions

scientific article published on 18 June 2016

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models

scientific article

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

scientific article

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions

scientific article published on 01 April 2008

Recent advances in implicit solvent-based methods for biomolecular simulations

scientific article published on 4 March 2008

Refinement of NMR structures using implicit solvent and advanced sampling techniques

scientific article published in December 2004

Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy

scientific article published on 19 September 2007

List of works by Charles L Brooks

A rapid solvent accessible surface area estimator for coarse grained molecular simulations

Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units

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

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins ⬇️

An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins

Application of solid-state NMR restraint potentials in membrane protein modeling

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

Constant-pH molecular dynamics using continuous titration coordinates

Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions

De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein

De novo prediction of the structures of M. tuberculosis membrane proteins

Evolution and physics in comparative protein structure modeling.

Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models

Exploring atomistic details of pH-dependent peptide folding

Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network

Force Field Influence on the Observation of π-Helical Protein Structures in Molecular Dynamics Simulations

Generalized born model with a simple smoothing function

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

Implicit solvation based on generalized Born theory in different dielectric environments

Improved model building and assessment of the Calcium-sensing receptor transmembrane domain

Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations

Linking folding with aggregation in Alzheimer's beta-amyloid peptides

Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations

Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

New analytic approximation to the standard molecular volume definition and its application to generalized born calculations

Novel generalized Born methods

PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions

Recent advances in implicit solvent-based methods for biomolecular simulations

Refinement of NMR structures using implicit solvent and advanced sampling techniques

Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy