Cargando…

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features

The virtual screening of large numbers of compounds against target protein binding sites has become an integral component of drug discovery workflows. This screening is often done by computationally docking ligands into a protein binding site of interest, but this has the drawback of a large number...

Descripción completa

Detalles Bibliográficos
Autores principales:	Holderbach, Stefan, Adam, Lukas, Jayaram, B., Wade, Rebecca C., Mukherjee, Goutam
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2020
Materias:	Molecular Biosciences
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7773945/ https://www.ncbi.nlm.nih.gov/pubmed/33392260 http://dx.doi.org/10.3389/fmolb.2020.601065

Ejemplares similares

Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands
por: Shao, Guangfeng, et al.
Publicado: (2021)

Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity
por: Korkuć, Paula, et al.
Publicado: (2015)

Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations
por: Rifai, Eko Aditya, et al.
Publicado: (2020)

Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches
por: Shin, Woong-Hee, et al.
Publicado: (2023)

Exploring Ligand Binding to Calcitonin Gene-Related Peptide Receptors
por: Deganutti, Giuseppe, et al.
Publicado: (2021)

Interplay Between Receptor-Ligand Binding and Lipid Domain Formation Depends on the Mobility of Ligands in Cell-Substrate Adhesion
por: Li, Long, et al.
Publicado: (2021)

The XBB.1.5 slightly increase the binding affinity for host receptor ACE2 and exhibit strongest immune escaping features: molecular modeling and free energy calculation
por: Suleman, Muhammad, et al.
Publicado: (2023)

Assessing the effect of forcefield parameter sets on the accuracy of relative binding free energy calculations
por: Sun, Shan, et al.
Publicado: (2022)

Ligand Binding Introduces Significant Allosteric Shifts in the Locations of Protein Fluctuations
por: Kumar, Ambuj, et al.
Publicado: (2021)

Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks
por: Ferruz, Noelia, et al.
Publicado: (2021)

Improving Small-Molecule Force Field Parameters in Ligand Binding Studies
por: Raniolo, Stefano, et al.
Publicado: (2021)

Big Data analytics for improved prediction of ligand binding and conformational selection
por: Gupta, Shivangi, et al.
Publicado: (2023)

Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments
por: Fernández-Quintero, Monica L., et al.
Publicado: (2020)

Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool
por: Karwounopoulos, Johannes, et al.
Publicado: (2022)

Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations
por: Alfonso-Prieto, Mercedes, et al.
Publicado: (2019)

Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective
por: Ahmad, Katya, et al.
Publicado: (2022)

Interplay of receptor-ligand binding and lipid domain formation during cell adhesion
por: Li, Long, et al.
Publicado: (2022)

Learned features of antibody-antigen binding affinity
por: Miller, Nathaniel L., et al.
Publicado: (2023)

An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models
por: Parks, Conor, et al.
Publicado: (2020)

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)

Changes in Protonation States of In-Pathway Residues can Alter Ligand Binding Pathways Obtained From Spontaneous Binding Molecular Dynamics Simulations
por: Girame, Helena, et al.
Publicado: (2022)

Regulation of Cholesterol Binding to the Receptor Patched1 by its interactions With the Ligand Sonic Hedgehog (Shh)
por: Zhong, Changqing, et al.
Publicado: (2022)

Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning
por: Miao, Yinglong, et al.
Publicado: (2023)

Enhancing response of a protein conformational switch by using two disordered ligand binding domains
por: Sekhon, Harsimranjit, et al.
Publicado: (2023)

Using Global Analysis to Extend the Accuracy and Precision of Binding Measurements with T cell Receptors and Their Peptide/MHC Ligands
por: Blevins, Sydney J., et al.
Publicado: (2017)

A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain
por: Panel, Nicolas, et al.
Publicado: (2017)

Theoretical Exploring Selective-Binding Mechanisms of JAK3 by 3D-QSAR, Molecular Dynamics Simulation and Free Energy Calculation
por: Zhu, Jingyu, et al.
Publicado: (2020)

Uncovering the Mechanism of Drug Resistance Caused by the T790M Mutation in EGFR Kinase From Absolute Binding Free Energy Calculations
por: Zhou, Huaxin, et al.
Publicado: (2022)

SiMeEx, a simplified method for metabolite extraction of adherent mammalian cells
por: Henne, Antonia, et al.
Publicado: (2022)

Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis
por: Wang, Qiantao, et al.
Publicado: (2015)

Structure of the Complete Dimeric Human GDAP1 Core Domain Provides Insights into Ligand Binding and Clustering of Disease Mutations
por: Nguyen, Giang Thi Tuyet, et al.
Publicado: (2021)

Fluorescence based HTS-compatible ligand binding assays for dopamine D(3) receptors in baculovirus preparations and live cells
por: Tahk, Maris-Johanna, et al.
Publicado: (2023)

DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor: Application to Spermine Synthase Enzyme
por: Peng, Yunhui, et al.
Publicado: (2019)

Erratum: Structure of the Complete Dimeric Human GDAP1 Core Domain Provides Insights Into Ligand Binding and Clustering of Disease Mutations
por: Tuyet Nguyen, Giang Thi, et al.
Publicado: (2022)

Erratum: DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor: Application to Spermine Synthase Enzyme
Publicado: (2019)

Molecular Mingling: Multimodal Predictions of Ligand Promiscuity in Pentameric Ligand-Gated Ion Channels
por: Koniuszewski, Filip, et al.
Publicado: (2022)

Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents
por: Chakravorty, Arghya, et al.
Publicado: (2018)

Recent Developments in Free Energy Calculations for Drug Discovery
por: King, Edward, et al.
Publicado: (2021)

Evidence for Quantum Chemical Effects in Receptor-Ligand Binding Between Integrin and Collagen Fragments — A Computational Investigation With an Impact on Tissue Repair, Neurooncolgy and Glycobiology
por: Eckert, Thomas, et al.
Publicado: (2021)

On Calculating Free Energy Differences Using Ensembles of Transition Paths
por: Hall, Robert, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_be3fuft1dv6od93ukseo6fsfj2