Cargando…

Comparison of Receptor–Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations

[Image: see text] Alchemical absolute binding free energy calculations are of increasing interest in drug discovery. These calculations require restraints between the receptor and ligand to restrict their relative positions and, optionally, orientations. Boresch restraints are commonly used, but the...

Descripción completa

Detalles Bibliográficos
Autores principales:	Clark, Finlay, Robb, Graeme, Cole, Daniel J., Michel, Julien
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	American Chemical Society 2023
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10308817/ https://www.ncbi.nlm.nih.gov/pubmed/37285579 http://dx.doi.org/10.1021/acs.jctc.3c00139

Ejemplares similares

Alchemical absolute protein–ligand binding free energies for drug design
por: Khalak, Y., et al.
Publicado: (2021)

Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations
por: Mey, Antonia S. J. S., et al.
Publicado: (2017)

Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes
por: Kilburg, Denise, et al.
Publicado: (2018)

How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations
por: Kaus, Joseph W., et al.
Publicado: (2015)

Dummy Atoms in Alchemical Free Energy Calculations
por: Fleck, Markus, et al.
Publicado: (2021)

Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease
por: Macchiagodena, Marina, et al.
Publicado: (2020)

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations
por: Aldeghi, Matteo, et al.
Publicado: (2016)

Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations
por: Bruce Macdonald, Hannah E., et al.
Publicado: (2018)

Optimization of Protein–Ligand Electrostatic Interactions Using an Alchemical Free-Energy Method
por: Wade, Alexander D., et al.
Publicado: (2019)

Alchemical Free-Energy Calculations of Watson–Crick and Hoogsteen Base Pairing Interconversion in DNA
por: Geronimo, Inacrist, et al.
Publicado: (2022)

Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors
por: Granadino-Roldán, José M., et al.
Publicado: (2019)

Uncertainty Quantification in Alchemical Free Energy Methods
por: Bhati, Agastya P., et al.
Publicado: (2018)

Effect of Atomic Charges on Octanol–Water Partition Coefficient Using Alchemical Free Energy Calculation
por: Ogata, Koji, et al.
Publicado: (2018)

Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation
por: Heinzelmann, Germano, et al.
Publicado: (2021)

Accurate calculation of the absolute free energy of binding for drug molecules
por: Aldeghi, Matteo, et al.
Publicado: (2016)

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations
por: Hauser, Kevin, et al.
Publicado: (2018)

Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations?
por: Procacci, Piero
Publicado: (2022)

Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers
por: Wu, Zhiyi, et al.
Publicado: (2022)

Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations
por: Stampolaki, Marianna, et al.
Publicado: (2023)

Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation
por: Rifai, Eko Aditya, et al.
Publicado: (2020)

Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder
por: Petrov, Drazen
Publicado: (2021)

Chemical Space Exploration with Active Learning and Alchemical Free Energies
por: Khalak, Yuriy, et al.
Publicado: (2022)

Modern Alchemical Free Energy Methods for Drug Discovery Explained
por: York, Darrin M.
Publicado: (2023)

Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex
por: La Serra, Maria Antonietta, et al.
Publicado: (2022)

Calculating the absolute binding free energy of the insulin dimer in an explicit solvent
por: Gong, Qiankun, et al.
Publicado: (2020)

Simulation of Reversible Protein–Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints
por: Perthold, Jan Walther, et al.
Publicado: (2017)

Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program
por: Wieder, Marcus, et al.
Publicado: (2022)

Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding
por: Bhati, Agastya P., et al.
Publicado: (2018)

High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2
por: Bhadane, Rajendra, et al.
Publicado: (2022)

Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica‐Exchange
por: Wan, Shunzhou, et al.
Publicado: (2019)

Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4
por: Guest, Ellen E., et al.
Publicado: (2022)

Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility
por: Wade, Alexander D., et al.
Publicado: (2022)

Absolute binding free energy calculations improve enrichment of actives in virtual compound screening
por: Feng, Mudong, et al.
Publicado: (2022)

RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology
por: Ries, Benjamin, et al.
Publicado: (2022)

Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations
por: Kaus, Joseph W., et al.
Publicado: (2015)

Predicting antibiotic resistance in complex protein targets using alchemical free energy methods
por: Brankin, Alice E., et al.
Publicado: (2022)

Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
por: Gapsys, Vytautas, et al.
Publicado: (2021)

Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and Its Inhibitors
por: Singh, Nidhi, et al.
Publicado: (2020)

Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs
por: Negami, Tatsuki, et al.
Publicado: (2019)

Computational scheme for pH‐dependent binding free energy calculation with explicit solvent
por: Lee, Juyong, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_j3dp9egg2mbe9lkplsp0vp5lq5