Cargando…

On Calculating Free Energy Differences Using Ensembles of Transition Paths

The free energy of a process is the fundamental quantity that determines its spontaneity or propensity at a given temperature. In particular, the binding free energy of a drug candidate to its biomolecular target is used as an objective quantity in drug design. Recently, binding kinetics—rates of as...

Descripción completa

Detalles Bibliográficos
Autores principales:	Hall, Robert, Dixon, Tom, Dickson, Alex
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/PMC7291376/ https://www.ncbi.nlm.nih.gov/pubmed/32582764 http://dx.doi.org/10.3389/fmolb.2020.00106

Ejemplares similares

Local Ion Densities can Influence Transition Paths of Molecular Binding
por: Roussey, Nicole M., et al.
Publicado: (2022)

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

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

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

Gibbs Free Energy Calculation of Mutation in PncA and RpsA Associated With Pyrazinamide Resistance
por: Khan, Muhammad Tahir, et al.
Publicado: (2020)

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

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)

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)

Integrative Conformational Ensembles of Sic1 Using Different Initial Pools and Optimization Methods
por: Gomes, Gregory-Neal W., et al.
Publicado: (2022)

Free Energy Profiles Relating With Conformational Transition of the Switch Domains Induced by G12 Mutations in GTP-Bound KRAS
por: Chen, Jianzhong, et al.
Publicado: (2022)

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)

Efficient and accurate diagnosis of otomycosis using an ensemble deep-learning model
por: Mao, Chenggang, et al.
Publicado: (2022)

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features
por: Holderbach, Stefan, et al.
Publicado: (2020)

Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery
por: McKay, Kyle, et al.
Publicado: (2022)

Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations
por: Fogolari, Federico, et al.
Publicado: (2018)

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

EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space
por: Wang, Zhenyu, et al.
Publicado: (2020)

Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein–Protein Docking Poses
por: Launay, Guillaume, et al.
Publicado: (2020)

Albumin Alters the Conformational Ensemble of Amyloid-β by Promiscuous Interactions: Implications for Amyloid Inhibition
por: Xie, Huisi, et al.
Publicado: (2021)

Aggregation-Prone Structural Ensembles of Transthyretin Collected With Regression Analysis for NMR Chemical Shift
por: Yang, Wonjin, et al.
Publicado: (2021)

How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case
por: Paissoni, Cristina, et al.
Publicado: (2021)

Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods
por: Ahmed, Mustapha Carab, et al.
Publicado: (2021)

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)

Transfer Free Energies of Test Proteins Into Crowded Protein Solutions Have Simple Dependence on Crowder Concentration
por: Nguemaha, Valery, et al.
Publicado: (2019)

Whole-Slide Image Analysis of Human Pancreas Samples to Elucidate the Immunopathogenesis of Type 1 Diabetes Using the QuPath Software
por: Apaolaza, Paola S., et al.
Publicado: (2021)

Missense Mutations Modify the Conformational Ensemble of the α-Synuclein Monomer Which Exhibits a Two-Phase Characteristic
por: Guzzo, Adrien, et al.
Publicado: (2021)

A Resource to Infer Molecular Paths Linking Cancer Mutations to Perturbation of Cell Metabolism
por: Iannuccelli, Marta, et al.
Publicado: (2022)

The permeation of potassium ions through the lipid scrambling path of the membrane protein nhTMEM16
por: Cheng, Xiaolu, et al.
Publicado: (2022)

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)

Multi-omics analysis: Paving the path toward achieving precision medicine in cancer treatment and immuno-oncology
por: Raufaste-Cazavieille, Virgile, et al.
Publicado: (2022)

Vitamin K Vitamers Differently Affect Energy Metabolism in IPEC-J2 Cells
por: Bernardini, Chiara, et al.
Publicado: (2021)

Known Evolutionary Paths Are Accessible to Engineered ß-Lactamases Having Altered Protein Motions at the Timescale of Catalytic Turnover
por: Alejaldre, Lorea, et al.
Publicado: (2020)

p53–GSDME Elevation: A Path for CDK7 Inhibition to Suppress Breast Cancer Cell Survival
por: Wang, Yueyuan, et al.
Publicado: (2021)

A Curvilinear-Path Umbrella Sampling Approach to Characterizing the Interactions Between Rapamycin and Three FKBP12 Variants
por: Joshi, Dhananjay C., et al.
Publicado: (2022)

First Principles Calculation of Protein–Protein Dimer Affinities of ALS-Associated SOD1 Mutants
por: Hsueh, Shawn C. C., et al.
Publicado: (2022)

Model-Free or Not?
por: Zumpfe, Kai, et al.
Publicado: (2021)

Quantitative Proteomic Analysis in Alveolar Type II Cells Reveals the Different Capacities of RAS and TGF-β to Induce Epithelial–Mesenchymal Transition
por: Zhou, Yilu, et al.
Publicado: (2021)

Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration
por: Chakraborty, Nabarun, et al.
Publicado: (2020)

A First Step Toward Unraveling the Energy Metabolism in Endurance Horses: Comparison of Plasma Nuclear Magnetic Resonance Metabolomic Profiles Before and After Different Endurance Race Distances
por: Le Moyec, Laurence, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_9e7ao5mc3rns4d3gdtuj5km1p0