ArticleJournal of chemical information and modeling2022
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA).
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.Journal of chemical information and modeling · 2026Article
- Molecular Dynamics Workflows to Compute Large-Scale Sets of Absolute Binding Free Energies Aiding Drug Candidate and Binding Pose Selection.Journal of chemical theory and computation · 2026Article
- MDCrow: automating molecular dynamics workflows with large language models.Machine learning: science and technology · 2026Article
- Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization.Journal of chemical information and modeling · 2026Article
- A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules.Journal of chemical information and modeling · 2026Article
- β-Carotene liposome-based responsive hydrogel inhibits palmitoylation to restore intracellular calcium homeostasis for effective periodontitis treatment.Journal of nanobiotechnology · 2025Article
- Towards precision epitopes based vaccine againstBiochemistry and biophysics reports · 2025Article
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 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
- Potential distribution theory of alchemical transfer.The Journal of chemical physics · 2025Article
- The Role of General Acid Catalysis in the Mechanism of an Alkyl Transferase Ribozyme.ACS catalysis · 2024Article
- Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach.Journal of chemical information and modeling · 2024Article
- Insights into the Gene Expression Profile of Classical Hodgkin Lymphoma: A Study towards Discovery of Novel Therapeutic Targets.Molecules (Basel, Switzerland) · 2024Article
- Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions.The journal of physical chemistry. B · 2024Article
- Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators.Journal of chemical information and modeling · 2024Article
- Alchemical Enhanced Sampling with Optimized Phase Space Overlap.Journal of chemical theory and computation · 2024Article
- What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling.Journal of chemical theory and computation · 2024Article
- Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- AmberTools.Journal of chemical information and modeling · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
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 Boost package that has been integrated into the AMBER22 release. The workflow establishes a flexible, end-to-end pipeline for performing alchemical free-energy simulations that brings to bear technologies, including new enhanced sampling features and analysis tools, to practical drug discovery problems. ProFESSA provides the user with top-level control of large sets of free-energy calculations and offers access to the following key functionalities: (1) automated setup of file infrastructure; (2) enhanced conformational and alchemical sampling with the ACES method; and (3) network-wide free-energy analysis with the optional imposition of cycle closure and experimental constraints. The workflow is applied to perform absolute and relative solvation free-energy and relative ligand-protein binding free-energy calculations using different atom-mapping procedures. Results demonstrate that the workflow is internally consistent and highly robust. Further, the application of a new network-wide Lagrange multiplier constraint analysis that imposes key experimental constraints substantially improves binding free-energy predictions.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.