ArticleJournal of chemical theory and computation2017
Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Elucidating the catalytic mechanism of a previously undescribed carbohydrate esterase family 7 acetyl xylan esterase (LaCE7A).The FEBS journal · 2026Article
- A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.Journal of chemical information and modeling · 2026Article
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- Comparative Analysis of Quantum-Mechanical and Standard Single-Structure Protein-Ligand Scoring Functions with MD-Based Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study.Journal of computer-aided molecular design · 2025Article
- FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks.Journal of chemical information and modeling · 2025Article
- Identification of naturally occurring drug-resistant mutations of SARS-CoV-2 papain-like protease.Nature communications · 2025Article
- apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods.The Journal of chemical physics · 2025Article
- Further exploration of the quantitative distance-energy and contact number-energy relationships for predicting the binding affinity of protein-ligand complexes.Biophysical journal · 2025Article
- Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations.Journal of chemical information and modeling · 2025Article
- The computationally guided design of selective targeters of multiple proteins (STaMPs) as a new opportunity for small molecule drug discovery.Frontiers in pharmacology · 2025Review
- Transformation of peptides to small molecules in medicinal chemistry: Challenges and opportunities.Acta pharmaceutica Sinica. B · 2024Review
- BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.Nature communications · 2024Article
- Development and test of highly accurate endpoint free energy methods. 3: partition coefficient prediction using a Poisson-Boltzmann method combined with a solvent accessible surface area model for SAMPL challenges.Physical chemistry chemical physics : PCCP · 2023Article
- Structure-based identification of novel inhibitors targeting the enoyl-ACP reductase enzyme of Acinetobacter baumannii.Scientific reports · 2023Article
- Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations.Journal of computer-aided molecular design · 2023Article
- Exploring the therapeutic mechanisms of Gleditsiae Spina acting on pancreatic cancerRSC advances · 2023Article
- Cooperative Substrate Binding Controls Catalysis in Bacterial Cytochrome P450terp (CYP108A1).Journal of the American Chemical Society · 2023Article
- ACES: Optimized Alchemically Enhanced Sampling.Journal of chemical theory and computation · 2023Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
We report the implementation of the thermodynamic integration method on the pmemd module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically delivers over 2 orders of magnitude of speed-up relative to a single CPU core for the calculation of ligand-protein binding affinities with no statistically significant numerical differences and thus provides a powerful new tool for drug discovery applications.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.