Ray Luo

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AmberTorchPB: A Unified Framework for PoissonBoltzmann-Based Reaction Field Energy Calculation via Tensor Computation
BPS2026 – Methodological considerations for MM-PBSA calculations of binding affinities in highly charged protein-protein systems: A systematic study
STK38/L promote tissue growth and cancer by inhibiting the Hippo pathway
Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization
DEGAUSS: A Novel Softcore Force Field Using Double Exponential van der Waals and Gaussian Charge for Molecular Dynamics Simulations I: Theory and Validation
End-to-End Modeling of Reaction Field Energy Using Data-Driven Geometric Graph Neural Networks
Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R
Grid-Context Convolutional Model for Efficient Molecular Surface Construction from Point Clouds
Isotropic Periodic Sum for Polarizable Gaussian Multipole Model
Modeling Molecular Recognition with the Polarizable Gaussian Multipole Model
Optimization of LennardJones Parameters for Induced Dipole Polarizable Gaussian Multipole Force Field
Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations
Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials
Role of artificial intelligence in revolutionizing drug discovery
Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model
End-to-end reaction field energy modeling via deep learning based voxel-to-voxel transform
Many-body effects in machine-learned molecular surface predictions
Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities
PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents
Shifting redox reaction equilibria on demand using an orthogonal redox cofactor
Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy
Understanding and fine-tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine
Computational approaches for the design of modulators targeting protein-protein interactions
Grid-Robust Efficient Neural Interface Model for Universal Molecule Surface Construction from Point Clouds
Novel breath biomarkers identification for early detection of hepatocellular carcinoma and cirrhosis using ML tools and GCMS
Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models
Recent Advances in Biomolecular Recognition
Streamlining and Optimizing Strategies of Electrostatic Parameterization
Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions
Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model
Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model
Advancing MM/PBSA calculations with machine learning and cuda GPUs
Development of polarizable Gaussian multipole model
Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform
Engineering Embden–Meyerhof–Parnas Glycolysis to Generate Noncanonical Reducing Power
Heparin-Assisted Amyloidogenesis Uncovered through Molecular Dynamics Simulations
Matrix-Augmented Pooling Strategy for High-Throughput Target Deconvolution Reveals Cell Type Specific Off-Targets and Responses
Motif-dependent immune co-receptor interactome profiling by photoaffinity chemical proteomics
Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase
PyRESP: A flexible program for polarizable force field parameterizations
PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields
Stress tensor and constant pressure simulation for polarizable Gaussian multipole model
The Hippo pathway kinases LATS1 and LATS2 attenuate cellular responses to heavy metals through phosphorylating MTF1
Development of a Pantetheine Force Field Library for Molecular Modeling
Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations
Growth-Based, High-Throughput Selection for NADH Preference in an Oxygen-Dependent Biocatalyst
Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulations
Recent Developments in Free Energy Calculations for Drug Discovery
Recent force field strategies for intrinsically disordered proteins
A 2,3-dialkoxynaphthalene-based naphthocage
Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations
An Oxetane-Based Polyketide Surrogate To Probe Substrate Binding in a Polyketide Synthase
Binding Induced Folding in p53-MDM2 Complex
Computational Analysis for the Rational Design of Anti-Amyloid Beta (A) Antibodies
Computational Studies of Intrinsically Disordered Proteins
Development of a High-Throughput, In Vivo Selection Platform for NADPH-Dependent Reactions Based on Redox Balance Principles
Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy
Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations
Engineering a Coenzyme A Detour To Expand the Product Scope and Enhance the Selectivity of the Ehrlich Pathway
Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins
In Vivo, High-Throughput Selection of Thermostable Cyclohexanone Monooxygenase (CHMO)
Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling
Leveraging Oxidative Stress to Regulate Redox Balance-Based, In Vivo Growth Selections for Oxygenase Engineering
Modeling Membrane ProteinLigand Binding Interactions: The Human Purinergic Platelet Receptor
Molecular Basis for Polyketide Ketoreductase–Substrate Interactions
Molecular Dynamics Simulations of p53 DNA-Binding Domain
New-Generation Amber United-Atom Force Field
Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis
The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins
Well-Balanced Force Field ff03CMAP for Folded and Disordered Proteins
An efficient second‐order poisson–boltzmann method
Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases
Dynamical important residue network (DIRN): network inference via conformational change
Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor
Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins
Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies
Improved Poisson–Boltzmann Methods for High-Performance Computing
Molecular basis for interactions between an acyl carrier protein and a ketosynthase
Polarizable Gaussian Multipole Framework for Electrostatic Interactions in Biomolecules
Improved Accuracy and Convergence of Intrinsically Disordered Protein Molecular Dynamics Simulations Using the ff14IDPSFF Force Field
Intrinsically disordered protein‐specific force field <scp>CHARMM</scp>36<scp>IDPSFF</scp>
Methods Supporting Information
Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB
Recent Developments and Applications of the MMPBSA Method
Regulation of the Hippo Pathway by Phosphatidic Acid-Mediated Lipid-Protein Interaction
Robustness and Efficiency of Poisson–Boltzmann Modeling on Graphics Processing Units
A Continuum Poisson–Boltzmann Model for Membrane Channel Proteins
Acceleration of Linear Finite-Difference Poisson–Boltzmann Methods on Graphics Processing Units
Correction: Conformation dynamics of the intrinsically disordered protein c-Myb with the ff99IDPs force field
Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode
Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid
Numerical interpretation of molecular surface field in dielectric modeling of solvation
ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins
Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network
Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis
Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions
Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch
Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis
A semi-implicit augmented IIM for Navier–Stokes equations with open, traction, or free boundary conditions
Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson–Boltzmann Equation
Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols
Recognition Mechanism between Lac Repressor and DNA with Correlation Network Analysis
Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis
Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins
Electrostatics and polarization effects in biophysical chemistry: in silico and in vitro
Molecular Dynamic Studies of the Reductase Domain of Polyketide Synthase from the Myxobacterium Stigmatella Aurantiaca
New force field on modeling intrinsically disordered proteins
Conformational Selection and Induced Fit in Specific Antibody and Antigen Recognition: SPE7 as a Case Study
Electrostatic forces in the Poisson-Boltzmann systems
Exploring a charge-central strategy in the solution of Poisson's equation for biomolecular applications
Exploring accurate Poisson–Boltzmann methods for biomolecular simulations
Numerical Poisson–Boltzmann model for continuum membrane systems
Atomistic Mechanism of MicroRNA Translation Upregulation via Molecular Dynamics Simulations
Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization
Dielectric pressure in continuum electrostatic solvation of biomolecules
Poisson–Boltzmann Implicit Solvation Models
Reducing Grid Dependence in Finite-Difference Poisson–Boltzmann Calculations
Annual Reports in Computational Chemistry
Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability
Dielectric boundary force in numerical Poisson–Boltzmann methods: Theory and numerical strategies
On-the-Fly Numerical Surface Integration for Finite-Difference Poisson–Boltzmann Methods
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Virtual screening using molecular simulations
A Revised Density Function for Molecular Surface Calculation in Continuum Solvent Models
AMBER11. University of California, San Francisco
Assessment of linear finite‐difference Poisson–Boltzmann solvers
Balancing Simulation Accuracy and Efficiency with the Amber United Atom Force Field
Exploring a coarse-grained distributive strategy for finite-difference Poisson–Boltzmann calculations
Quantitative analysis of Poisson–Boltzmann implicit solvent in molecular dynamics
Achieving energy conservation in Poisson–Boltzmann molecular dynamics: Accuracy and precision with finite-difference algorithms
Molecular mechanisms of functional rescue mediated by P53 tumor suppressor mutations
On removal of charge singularity in Poisson–Boltzmann equation
Performance of Nonlinear Finite-Difference Poisson−Boltzmann Solvers
Roles of Boundary Conditions in DNA Simulations: Analysis of Ion Distributions with the Finite-Difference Poisson-Boltzmann Method
Structural and functional implications of p53 missense cancer mutations
All-Atom Computer Simulations of Amyloid Fibrils Disaggregation
Continuum Polarizable Force Field within the Poisson−Boltzmann Framework
Hydrogen-Bonded Complexes in Chloroform: Affinity, Entropy, and Conformation
Impact of low-frequency hotspot mutation R282Q on the structure of p53 DNA-binding domain as revealed by crystallography at 1.54 Å resolution
Inhibition Kinetics and Emodin Cocrystal Structure of a Type II Polyketide Ketoreductase,
Poisson-Boltzmann Solvents in Molecular Dynamics Simulations
Protein Stability Prediction: A Poisson−Boltzmann Approach
AMBER5; University of California: San Francisco, CA
Continuum treatment of electronic polarization effect
Implicit Nonpolar Solvent Models
Force field influences in β‐hairpin folding simulations
How Well Does Poisson−Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis
Is Poisson-Boltzmann theory insufficient for protein folding simulations?
Computational prediction of p53 rescue; Effects of second-site rescue mutations on the stability of cancer mutants
Nonpolar implicit solvent models
Overcoming entropic barrier with coupled sampling at dual resolutions
The Amber biomolecular simulation programs
Enhanced ab initio protein folding simulations in Poisson–Boltzmann molecular dynamics with self-guiding forces
Interplay of secondary structures and side-chain contacts in the denatured state of BBA1
Physical scoring function based on AMBER force field and Poisson–Boltzmann implicit solvent for protein structure prediction
A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations
A Poisson–Boltzmann dynamics method with nonperiodic boundary condition
From 1D to 3D: Cooperative Determination of a Protein’s Structure from its Sequence
Accelerated Poisson–Boltzmann calculations for static and dynamic systems
An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis
Interpreting trends in the binding of cyclic ureas to HIV-1 protease
Ligand-receptor docking with the Mining Minima optimizer
The Physical Basis of Nucleic Acid Base Stacking in Water
Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease
Modeling Molecular Recognition: Theory and Application
Synthetic Adenine Receptors: Direct Calculation of Binding Affinity and Entropy
Calculation of the binding affinity of phenylalanine to beta-cyclodextrin
Computational Study of KNI-272, a Potent Inhibitor of HIV-1 Protease: On the Mechanism of Preorganization
Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation
Strength of Solvent-Exposed Salt-Bridges
PROSTAR: The protein potential test site