Ray Luo Lab

Contact

Fri, 05 Jun 2026 00:00:00 +0000

People

Fri, 05 Jun 2026 00:00:00 +0000

Polarizable Gaussian Multipole force field

Fri, 05 Jun 2026 00:00:00 +0000

We develop the polarizable Gaussian Multipole (pGM) model — a physically motivated force field in which atomic charges and multipoles are represented by smooth Gaussian distributions. Our work spans electrostatic parameterization (PyRESP, PCMRESP), refinement of atomic polarizabilities, energy-conserving induced-dipole schemes, periodic-boundary electrostatics via the isotropic periodic sum, and stress/pressure control for accurate condensed-phase molecular dynamics.

Machine learning for molecular surfaces and implicit solvent

Thu, 04 Jun 2026 00:00:00 +0000

We bring machine learning to implicit-solvent modeling: graph and convolutional neural networks that learn the solvent-excluded molecular surface, and data-driven models of Poisson–Boltzmann reaction-field energies. Implemented on GPUs (AmberTorchPB), these methods make continuum electrostatics fast and smooth enough for routine biomolecular simulation.

Binding free energies — MM/PBSA and alchemical methods

Wed, 03 Jun 2026 00:00:00 +0000

We develop methods to predict binding free energies for drug discovery: GPU-accelerated MM/PBSA for protein–ligand and membrane-protein systems, and alchemical free-energy perturbation made robust by singularity-free softcore potentials (DEGAUSS). The goal is accurate, efficient affinity prediction across diverse targets.

Allostery and disease-relevant protein dynamics

Tue, 02 Jun 2026 00:00:00 +0000

We use molecular dynamics and free-energy analysis to uncover cryptic allosteric sites and to interpret disease-associated mutations in signaling proteins and cancer targets (for example SHP2 and the Hippo-pathway kinases), connecting conformational dynamics to function and therapeutic opportunity.

AmberTorchPB: A Unified Framework for PoissonBoltzmann-Based Reaction Field Energy Calculation via Tensor Computation

Thu, 01 Jan 2026 00:00:00 +0000

BPS2026 – Methodological considerations for MM-PBSA calculations of binding affinities in highly charged protein-protein systems: A systematic study

Thu, 01 Jan 2026 00:00:00 +0000

STK38/L promote tissue growth and cancer by inhibiting the Hippo pathway

Thu, 01 Jan 2026 00:00:00 +0000

Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization

Wed, 01 Jan 2025 00:00:00 +0000

DEGAUSS: A Novel Softcore Force Field Using Double Exponential van der Waals and Gaussian Charge for Molecular Dynamics Simulations I: Theory and Validation

Wed, 01 Jan 2025 00:00:00 +0000

End-to-End Modeling of Reaction Field Energy Using Data-Driven Geometric Graph Neural Networks

Wed, 01 Jan 2025 00:00:00 +0000

Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R

Wed, 01 Jan 2025 00:00:00 +0000

Grid-Context Convolutional Model for Efficient Molecular Surface Construction from Point Clouds

Wed, 01 Jan 2025 00:00:00 +0000

Isotropic Periodic Sum for Polarizable Gaussian Multipole Model

Wed, 01 Jan 2025 00:00:00 +0000

Modeling Molecular Recognition with the Polarizable Gaussian Multipole Model

Wed, 01 Jan 2025 00:00:00 +0000

Optimization of LennardJones Parameters for Induced Dipole Polarizable Gaussian Multipole Force Field

Wed, 01 Jan 2025 00:00:00 +0000

Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations

Wed, 01 Jan 2025 00:00:00 +0000

Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials

Wed, 01 Jan 2025 00:00:00 +0000

Role of artificial intelligence in revolutionizing drug discovery

Wed, 01 Jan 2025 00:00:00 +0000

Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model

Mon, 01 Jan 2024 00:00:00 +0000

End-to-end reaction field energy modeling via deep learning based voxel-to-voxel transform

Mon, 01 Jan 2024 00:00:00 +0000

Many-body effects in machine-learned molecular surface predictions

Mon, 01 Jan 2024 00:00:00 +0000

Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities

Mon, 01 Jan 2024 00:00:00 +0000

PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents

Mon, 01 Jan 2024 00:00:00 +0000

Shifting redox reaction equilibria on demand using an orthogonal redox cofactor

Mon, 01 Jan 2024 00:00:00 +0000

Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy

Mon, 01 Jan 2024 00:00:00 +0000

Understanding and fine-tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine

Mon, 01 Jan 2024 00:00:00 +0000

Computational approaches for the design of modulators targeting protein-protein interactions

Sun, 01 Jan 2023 00:00:00 +0000

Grid-Robust Efficient Neural Interface Model for Universal Molecule Surface Construction from Point Clouds

Sun, 01 Jan 2023 00:00:00 +0000

Novel breath biomarkers identification for early detection of hepatocellular carcinoma and cirrhosis using ML tools and GCMS

Sun, 01 Jan 2023 00:00:00 +0000

Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models

Sun, 01 Jan 2023 00:00:00 +0000

Recent Advances in Biomolecular Recognition

Sun, 01 Jan 2023 00:00:00 +0000

Streamlining and Optimizing Strategies of Electrostatic Parameterization

Sun, 01 Jan 2023 00:00:00 +0000

Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions

Sun, 01 Jan 2023 00:00:00 +0000

Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model

Sun, 01 Jan 2023 00:00:00 +0000

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

Sat, 01 Jan 2022 00:00:00 +0000

Advancing MM/PBSA calculations with machine learning and cuda GPUs

Sat, 01 Jan 2022 00:00:00 +0000

Development of polarizable Gaussian multipole model

Sat, 01 Jan 2022 00:00:00 +0000

Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform

Sat, 01 Jan 2022 00:00:00 +0000

Engineering Embden–Meyerhof–Parnas Glycolysis to Generate Noncanonical Reducing Power

Sat, 01 Jan 2022 00:00:00 +0000

Heparin-Assisted Amyloidogenesis Uncovered through Molecular Dynamics Simulations

Sat, 01 Jan 2022 00:00:00 +0000

Matrix-Augmented Pooling Strategy for High-Throughput Target Deconvolution Reveals Cell Type Specific Off-Targets and Responses

Sat, 01 Jan 2022 00:00:00 +0000

Motif-dependent immune co-receptor interactome profiling by photoaffinity chemical proteomics

Sat, 01 Jan 2022 00:00:00 +0000

Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase

Sat, 01 Jan 2022 00:00:00 +0000

PyRESP: A flexible program for polarizable force field parameterizations

Sat, 01 Jan 2022 00:00:00 +0000

PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields

Sat, 01 Jan 2022 00:00:00 +0000

Stress tensor and constant pressure simulation for polarizable Gaussian multipole model

Sat, 01 Jan 2022 00:00:00 +0000

The Hippo pathway kinases LATS1 and LATS2 attenuate cellular responses to heavy metals through phosphorylating MTF1

Sat, 01 Jan 2022 00:00:00 +0000

Allostery in molecular recognition

Wed, 06 Jan 2021 00:00:00 +0000

Mechanisms of allosteric regulation in molecular recognition, studied with explicit-solvent molecular dynamics and MMPBSA post-analysis.

Force fields for intrinsically disordered proteins

Mon, 04 Jan 2021 00:00:00 +0000

Computational models and tools to characterize intrinsically disordered proteins, integrating molecular dynamics with NMR measurements.

MMPBSA for membrane proteins

Sun, 03 Jan 2021 00:00:00 +0000

Extending MMPBSA protein–ligand binding-affinity calculations to membrane proteins, with and without channels.

GPU Poisson–Boltzmann modeling

Sat, 02 Jan 2021 00:00:00 +0000

Linear and nonlinear finite-difference Poisson–Boltzmann (FDPB) solvers for the NVIDIA CUDA platform.

Development of a Pantetheine Force Field Library for Molecular Modeling

Fri, 01 Jan 2021 00:00:00 +0000

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

Fri, 01 Jan 2021 00:00:00 +0000

Growth-Based, High-Throughput Selection for NADH Preference in an Oxygen-Dependent Biocatalyst

Fri, 01 Jan 2021 00:00:00 +0000

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

Fri, 01 Jan 2021 00:00:00 +0000

Recent Developments in Free Energy Calculations for Drug Discovery

Fri, 01 Jan 2021 00:00:00 +0000

Recent force field strategies for intrinsically disordered proteins

Fri, 01 Jan 2021 00:00:00 +0000

A 2,3-dialkoxynaphthalene-based naphthocage