Cargando…

Application of the ESMACS Binding Free Energy Protocol to a Multi‐Binding Site Lactate Dehydogenase A Ligand Dataset

Over the past two decades, the use of fragment‐based lead generation has become a common, mature approach to identify tractable starting points in chemical space for the drug discovery process. This approach naturally involves the study of the binding properties of highly heterogeneous ligands. Such...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wright, David W., Husseini, Fouad, Wan, Shunzhou, Meyer, Christophe, van Vlijmen, Herman, Tresadern, Gary, Coveney, Peter V.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	John Wiley and Sons Inc. 2019
Materias:	Full Papers
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8438761/ https://www.ncbi.nlm.nih.gov/pubmed/34553124 http://dx.doi.org/10.1002/adts.201900194

Ejemplares similares

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4
por: Wright, David W., et al.
Publicado: (2019)

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

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase
por: Wan, Shunzhou, et al.
Publicado: (2022)

Large scale relative protein ligand binding affinities using non-equilibrium alchemy
por: Gapsys, Vytautas, et al.
Publicado: (2019)

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors
por: Wan, Shunzhou, et al.
Publicado: (2020)

Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation
por: Pérez-Benito, Laura, et al.
Publicado: (2018)

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction
por: Wan, Shunzhou, et al.
Publicado: (2020)

Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations
por: Voice, Angus T., et al.
Publicado: (2021)

Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions
por: Wan, Shunzhou, et al.
Publicado: (2023)

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 binding affinity calculations at extreme scales
por: Dakka, Jumana, et al.
Publicado: (2018)

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase
por: Talibov, Vladimir O., et al.
Publicado: (2021)

Quadruplex–Duplex Junction: A High‐Affinity Binding Site for Indoloquinoline Ligands
por: Vianney, Yoanes Maria, et al.
Publicado: (2020)

TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing
por: Bieniek, Mateusz K., et al.
Publicado: (2021)

Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease
por: Wan, Shunzhou, et al.
Publicado: (2021)

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
por: Gapsys, Vytautas, et al.
Publicado: (2022)

The effect of protein mutations on drug binding suggests ensuing personalised drug selection
por: Wan, Shunzhou, et al.
Publicado: (2021)

Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study
por: Wan, Shunzhou, et al.
Publicado: (2016)

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

TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
por: Bieniek, Mateusz K., et al.
Publicado: (2023)

Comprehensive 3D‐RISM analysis of the hydration of small molecule binding sites in ligand‐free protein structures
por: Yoshidome, Takashi, et al.
Publicado: (2020)

Monte Carlo simulations using PELE to identify a protein–protein inhibitor binding site and pose
por: Díaz, Lucía, et al.
Publicado: (2020)

Influence of length and flexibility of spacers on the binding affinity of divalent ligands
por: Liese, Susanne, et al.
Publicado: (2015)

Ligand binding and global adaptation of the GlnPQ substrate binding domain 2 revealed by molecular dynamics simulations
por: Kienlein, Maximilian, et al.
Publicado: (2020)

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups
por: Rafieiolhosseini, Neda, et al.
Publicado: (2022)

Thermodynamic coupling between neighboring binding sites in homo‐oligomeric ligand sensing proteins from mass resolved ligand‐dependent population distributions
por: Li, Weicheng, et al.
Publicado: (2022)

Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level
por: Olsson, Martin A., et al.
Publicado: (2016)

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
por: Lenselink, Eelke B., et al.
Publicado: (2016)

Influencing the Self‐Sorting Behavior of [2.2]Paracyclophane‐Based Ligands by Introducing Isostructural Binding Motifs
por: Volbach, Lucia, et al.
Publicado: (2020)

MS Binding Assays for Glycine Transporter 2 (GlyT2) Employing Org25543 as Reporter Ligand
por: Ackermann, Thomas M., et al.
Publicado: (2020)

Molecular blueprint of allosteric binding sites in a homologue of the agonist-binding domain of the α7 nicotinic acetylcholine receptor
por: Spurny, Radovan, et al.
Publicado: (2015)

Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses
por: Wienen‐Schmidt, Barbara, et al.
Publicado: (2020)

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software
por: Khalak, Yuriy, et al.
Publicado: (2020)

Salt-mediated two-site ligand binding by the cocaine-binding aptamer
por: Neves, Miguel A.D., et al.
Publicado: (2017)

Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation
por: Reif, Maria M, et al.
Publicado: (2014)

PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
por: Ammar, Ammar, et al.
Publicado: (2023)

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols
por: Bhati, Agastya P., et al.
Publicado: (2022)

Large-scale binding affinity calculations on commodity compute clouds
por: Zasada, S. J., et al.
Publicado: (2020)

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding
por: Barnett, Christopher B, et al.
Publicado: (2020)

Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes
por: Manna, Sudeshna, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_0u28rp80dd8lr6lk5q3fvajkre