Tai‐Sung Lee
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View article: SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations
SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations Open
Accurate and efficient calculation of alchemical free energies is a critical challenge in computational chemistry, frequently hindered by the inherent limitations of conventional thermodynamic integration (TI) methods. These limitations in…
View article: Recent Developments in Amber Biomolecular Simulations
Recent Developments in Amber Biomolecular Simulations Open
Amber is a molecular dynamics (MD) software package first conceived by Peter Kollman, his lab and collaborators to simulate biomolecular systems. The pmemd module is available as a serial version for central processing units (CPUs), NVIDIA…
View article: ABCG2: A Milestone Charge Model for Accurate Solvation Free Energy Calculation
ABCG2: A Milestone Charge Model for Accurate Solvation Free Energy Calculation Open
In this report, we describe the development and validation of ABCG2, a new charge model with milestone free energy accuracy, while allowing instantaneous atomic charge assignment for arbitrary organic molecules. In combination with the sec…
View article: Impact of Timestep on Energy Drift and Accuracy of Alchemical Free Energy Calculations
Impact of Timestep on Energy Drift and Accuracy of Alchemical Free Energy Calculations Open
Molecular dynamics (MD) simulations are essential for investigating complex bi- ological systems. Timestep selection is crucial for accuracy and efficiency, yet the common practice of using a 4 fs timestep with hydrogen mass repartitioning…
View article: Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach Open
Accurate in silico predictions of how strongly small molecules bind to proteins, such as those afforded by relative binding free energy (RBFE) calculations, can greatly increase the efficiency of the hit-to-lead and lead optimization stage…
View article: Alchemical Enhanced Sampling with Optimized Phase Space Overlap
Alchemical Enhanced Sampling with Optimized Phase Space Overlap Open
An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate importance sampling in free energy simulations. The method achieves enhanced sampling from Hamiltonian replica exchange within a dual topology framewo…
View article: AmberTools
AmberTools Open
AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
View article: ACES: Optimized Alchemically Enhanced Sampling
ACES: Optimized Alchemically Enhanced Sampling Open
We present an alchemical enhanced sampling (ACES) method implemented in the GPU-accelerated AMBER free energy MD engine. The methods hinges on the creation of an "enhanced sampling state" by reducing or eliminating selected potential energ…
View article: AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways
AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways Open
We develop a framework for the design of optimized alchemical transformation pathways in free energy simulations using nonlinear mixing and a new functional form for so-called "softcore" potentials. We describe the implementation and testi…
View article: AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA)
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA) Open
We report an automated workflow for production free-energy simulation setup and analysis (ProFESSA) using the GPU-accelerated AMBER free-energy engine with enhanced sampling features and analysis tools, part of the AMBER Drug Discovery Boo…
View article: CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER Open
Alchemical free energy methods, such as free energy perturbation (FEP) and thermodynamic integration (TI), become increasingly popular and crucial for drug design and discovery. However, the system preparation of alchemical free energy sim…
View article: Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost
Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost Open
Recent concurrent advances in methodology development, computer hardware and simulation software has transformed our ability to make practical, quantitative predictions of relative ligand binding affinities to guide rational drug design. I…
View article: Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost
Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost Open
Recent concurrent advances in methodology development, computer hardware and simulation software has transformed our ability to make practical, quantitative predictions of relative ligand binding affinities to guide rational drug design. I…
View article: Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies
Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies Open
In silico screening of drug-target interactions is a key part of the drug discovery process. Changes in the drug scaffold via contraction or expansion of rings, the breaking of rings, and the introduction of cyclic structures from acyclic …
View article: Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies
Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies Open
In silico screening of drug target interactions is a key part of the drug discovery process. Changes in the drug scaffold via contraction or expansion of rings, the breaking of rings and the introduction of cyclic structures from acyclic s…
View article: Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies
Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies Open
In silico screening of drug target interactions is a key part of the drug discovery process. Changes in the drug scaffold via contraction or expansion of rings, the breaking of rings and the introduction of cyclic structures from acyclic s…
View article: A fast and high-quality charge model for the next generation general AMBER force field
A fast and high-quality charge model for the next generation general AMBER force field Open
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the world to perform in silico simulations and modelings on diverse scientific topics, especially in the field of computer-aided drug design whose primary t…
View article: Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery Open
Predicting protein-ligand binding affinities and the associated thermodynamics of biomolecular recognition is a primary objective of structure-based drug design. Alchemical free energy simulations offer a highly accurate and computationall…
View article: Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials
Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials Open
Progress in the development of GPU-accelerated free energy simulation software has enabled practical applications on complex biological systems and fueled efforts to develop more accurate and robust predictive methods. In particular, this …
View article: Validation of Free Energy Methods in AMBER
Validation of Free Energy Methods in AMBER Open
Herein we provide high-precision validation tests of the latest GPU-accelerated free energy code in AMBER. We demonstrate that consistent free energy results are obtained in both the gas phase and in solution. We first show, in the context…
View article: Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein–Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF
Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein–Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF Open
Accurate prediction of the absolute or relative protein-ligand binding affinity is one of the major tasks in computer-aided drug design projects, especially in the stage of lead optimization. In principle, the alchemical free energy (AFE) …
View article: Using AMBER18 for Relative Free Energy Calculations
Using AMBER18 for Relative Free Energy Calculations Open
With renewed interest in free energy methods in contemporary structure-based drug design, there is a pressing need to validate against multiple targets and force fields to assess the overall ability of these methods to accurately predict r…
View article: Validation of AMBER/GAFF for Relative Free Energy Calculations
Validation of AMBER/GAFF for Relative Free Energy Calculations Open
We computed relative binding free energies using GPU accelerated Thermodynamic Integration (GPU-TI) on a dataset originally assembled by Schrödinger, Inc.. Using their GPU enabled free energy code (FEP+) and the OPLS2.1 force field combine…
View article: Validation of AMBER/GAFF for Relative Free Energy Calculations
Validation of AMBER/GAFF for Relative Free Energy Calculations Open
We computed relative binding free energies using GPU accelerated Thermodynamic Integration (GPU-TI) on a dataset originally assembled by Schrödinger, Inc.. Using their GPU enabled free energy code (FEP+) and the OPLS2.1 force field combine…
View article: GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features Open
We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber18. Of particular interest is the development of alchemical free energy algorithms, including free energy perturbation and …
View article: A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations
A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations Open
The computational efficiency of approximate quantum mechanical methods allows their use for the construction of multidimensional reaction free energy profiles. It has recently been demonstrated that quantum models based on the neglect of d…
View article: RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations Open
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. RE simulations involve the concurrent execution of independent simulations which infrequently interact and exchange information. Th…