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List of works by Ray Luo

<i>PyRESP</i>: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields

scientific article published on 10 May 2022

A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.

scientific article published on 31 May 2017

A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation

scientific article published on November 2014

A Poisson–Boltzmann dynamics method with nonperiodic boundary condition

article

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

scientific article (publication date: December 2003)

A revised density function for molecular surface definition in continuum solvent models

scientific article

A semi-implicit augmented IIM for Navier-Stokes equations with open, traction, or free boundary conditions.

scientific article published on 19 May 2015

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

scientific article published in October 2002

Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units.

scientific article

Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model

scientific article published in 2022

Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics: Accuracy and Precision with Finite-Difference Algorithms

scientific article published on January 2009

All-atom computer simulations of amyloid fibrils disaggregation

scientific article published on 29 August 2008

Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations.

scientific article

Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network

scientific article published on 14 November 2016

An Oxetane-Based Polyketide Surrogate To Probe Substrate Binding in a Polyketide Synthase.

scientific article published on 5 April 2018

An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis.

scientific article

An efficient second-order poisson-boltzmann method

scientific article published on 18 February 2019

Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation

scientific article published on 21 September 2015

Assessment of linear finite-difference Poisson-Boltzmann solvers

scientific article

Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations

scientific article

Balancing simulation accuracy and efficiency with the Amber united atom force field

scientific article published in March 2010

Binding induced folding in p53-MDM2 complex

scientific article published on 16 February 2007

Biological applications of classical electrostatics methods

Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis

scientific article

Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions

scientific article published on 4 May 2016

Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols

scientific article

Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aβ) Antibodies

scientific article published on 16 April 2018

Computational Studies of Intrinsically Disordered Proteins

scientific article published on 08 November 2018

Conformation Dynamics of the Intrinsically Disordered Protein c-Myb with the ff99IDPs Force Field

scientific article published on 7 June 2017

Conformational selection and induced fit in specific antibody and antigen recognition: SPE7 as a case study

scientific article published on 12 April 2013

Confronting the problem of interconnected structural changes in the comparative modeling of proteins.

scientific article published on November 1995

Continuum polarizable force field within the Poisson-Boltzmann framework

scientific article published on 29 May 2008

Continuum treatment of electronic polarization effect

scientific article published in March 2007

Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode

scientific article published on 11 January 2017

Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy

scientific article published on 04 February 2019

Development of a High-Throughput, In Vivo Selection Platform for NADPH-Dependent Reactions Based on Redox Balance Principles

Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability

scientific article published on 10 March 2011

Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies

scientific article

Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes

scientific article published on 5 July 2012

Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization

scientific article

Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies

scientific article published on October 2011

Dielectric pressure in continuum electrostatic solvation of biomolecules

scientific article published on 23 October 2012

Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch

scientific article published on 03 August 2016

Editorial

Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations

scientific article published on 01 September 2020

Electrostatic forces in the Poisson-Boltzmann systems

scientific article

Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor

scientific article published on 29 November 2019

Engineering a Coenzyme A Detour To Expand the Product Scope and Enhance the Selectivity of the Ehrlich Pathway

scientific article published on 20 November 2018

Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces

scientific article published in May 2004

Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins

scientific article published on 07 April 2020

Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations

scientific article published on 25 March 2021

Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications

scientific article

Exploring a coarse-grained distributive strategy for finite-difference Poisson-Boltzmann calculations

scientific article

Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.

scientific article published in December 2017

Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.

scientific article published on November 2013

Force field influences in beta-hairpin folding simulations

scientific article

Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants.

scientific article published on April 2006

Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies

scientific article published on 13 June 2019

How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis

scientific article

Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 Å resolution

scientific article

Implicit nonpolar solvent models

scientific article published on 5 October 2007

Improved Poisson-Boltzmann Methods for High-Performance Computing

scientific article published on 30 September 2019

Inhibition Kinetics and Emodin Cocrystal Structure of a Type II Polyketide Ketoreductase † , ‡

scientific article

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

Interpreting trends in the binding of cyclic ureas to HIV-1 protease.

scientific article published in June 2001

Intrinsically disordered protein-specific force field CHARMM36IDPSFF

scientific article published on 01 July 2018

Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling

scientific article published on 22 November 2017

Is Poisson-Boltzmann theory insufficient for protein folding simulations?

scientific article published in January 2006

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

scientific article

Ligand-receptor docking with the Mining Minima optimizer

scientific article published in February 2001

Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations

scientific article published on 13 September 2021

Modeling Membrane Protein-Ligand Binding Interactions: The Human Purinergic Platelet Receptor

scientific article

Modeling molecular recognition: theory and application

scientific article published on January 2000

Molecular Basis for Polyketide Ketoreductase-Substrate Interactions

scientific article published on 13 October 2020

Molecular dynamics simulations of p53 DNA-binding domain

scientific article published on 8 September 2007

Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations

scientific article published on September 2009

New force field on modeling intrinsically disordered proteins.

scientific article

New-generation amber united-atom force field

scientific article published in July 2006

Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation

scientific article published in April 1999

Numerical Poisson-Boltzmann Model for Continuum Membrane Systems.

scientific article published on 7 November 2012

Numerical interpretation of molecular surface field in dielectric modeling of solvation

scientific article published on 20 March 2017

On removal of charge singularity in Poisson-Boltzmann equation.

scientific article

On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods

scientific article

Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB

scientific article published on 01 June 2018

Overcoming entropic barrier with coupled sampling at dual resolutions

scientific article published in November 2005

Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers

scientific article

Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction.

scientific article

Poisson–Boltzmann Implicit Solvation Models

article

Protein stability prediction: a Poisson-Boltzmann approach

scientific article published on 23 January 2008

Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics

scientific article published on 23 December 2009

Recent Developments and Applications of the MMPBSA Method

scientific article

Recent progress in adapting Poisson–Boltzmann methods to molecular simulations

Recognition Mechanism between Lac Repressor and DNA with Correlation Network Analysis

article

Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations

scientific article published on 18 June 2012

Regulation of the Hippo Pathway by Phosphatidic Acid-Mediated Lipid-Protein Interaction

scientific article published on 04 October 2018

Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units

scientific article published on 31 December 2018

Roles of boundary conditions in DNA simulations: analysis of ion distributions with the finite-difference Poisson-Boltzmann method

scientific article published on July 2009

Specific Recognition Mechanism between RNA and the KH3 Domain of Nova-2 Protein

Stress tensor and constant pressure simulation for polarizable Gaussian multipole model

scientific article published in 2022

Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis

scientific article

Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis

scientific article published on 26 May 2016

Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis

scientific article published on 15 April 2016

Synthetic Adenine Receptors: Direct Calculation of Binding Affinity and Entropy

scientific article published in 2000

Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins

scientific article

The Amber biomolecular simulation programs

scientific article (publication date: December 2005)

The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins

scientific article published on 27 April 2017

Virtual screening using molecular simulations

scientific article

Well-Balanced Force Field ff03CMAP for Folded and Disordered Proteins

scientific article published on 04 November 2019

Widespread but small-scale changes in the structural and dynamic properties of vaccinia virus poly(A) polymerase upon association with its processivity factor in solution

scientific article

ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins

scientific article

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