List of works - Bernard R Brooks

A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations

scientific article published on 01 August 2020

Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

scientific article published on 30 September 2016

Albumin-chaperoned cyanine dye yields superbright NIR-II fluorophore with enhanced pharmacokinetics

scientific article published on 13 September 2019

Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer's Aβ Protofilaments

scientific article published on 29 November 2018

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

scientific article published on 12 January 2017

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations

scientific article published on 22 August 2016

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections

scientific article published on 19 September 2016

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

scientific article published on 06 December 2021

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge

scientific article published on 30 August 2016

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics

scientific article published on 5 January 2016

Comparative study of various normal mode analysis techniques based on partial Hessians

scientific article

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges

scientific article published on 15 October 2018

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

scientific article published on 23 November 2015

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

scientific article published on 15 August 2014

Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations

scientific article published on 28 October 2020

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian

scientific article published on 6 January 2011

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level

scientific article published on 21 September 2017

Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale

scientific article published on 01 October 2018

Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins

scientific article published on 01 June 2018

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

scientific article published on 30 October 2014

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions

scientific article published on 18 May 2015

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

scientific article

Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method

scientific article published on 06 August 2018

Protein p<i>K</i><sub>a</sub> Prediction by Tree-Based Machine Learning

scientific article published on 15 March 2022

Reformulation of the self-guided molecular simulation method

scientific article published on 01 September 2020

Structural Modulation of Human Amylin Protofilaments by Naturally-Occurring Mutations

scientific article

The Extended Eighth‐Shell method for periodic boundary conditions with rotational symmetry

scientific article published on 12 May 2021

The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation

scientific article published on 01 June 2019

List of works by Bernard R Brooks

A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations

Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

Albumin-chaperoned cyanine dye yields superbright NIR-II fluorophore with enhanced pharmacokinetics

Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer's Aβ Protofilaments

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics

Comparative study of various normal mode analysis techniques based on partial Hessians

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level

Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale

Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method

Protein p<i>K</i><sub>a</sub> Prediction by Tree-Based Machine Learning

Reformulation of the self-guided molecular simulation method

Structural Modulation of Human Amylin Protofilaments by Naturally-Occurring Mutations

The Extended Eighth‐Shell method for periodic boundary conditions with rotational symmetry

The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation