Cargando…

Large-scale application of free energy perturbation calculations for antibody design

Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate the free energy difference between distinct chemical systems. Here we report our implementation of automated large-scale FEP calculations, using the Amber software package, to facilitate antibody design and e...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zhu, Fangqiang, Bourguet, Feliza A., Bennett, William F. D., Lau, Edmond Y., Arrildt, Kathryn T., Segelke, Brent W., Zemla, Adam T., Desautels, Thomas A., Faissol, Daniel M.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2022
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9302960/ https://www.ncbi.nlm.nih.gov/pubmed/35864134 http://dx.doi.org/10.1038/s41598-022-14443-z

Ejemplares similares

Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1
por: Clark, Anthony J., et al.
Publicado: (2017)

Assessing the stability of free-energy perturbation calculations by performing variations in the method
por: Manzoni, Francesco, et al.
Publicado: (2018)

Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants
por: Desautels, Thomas A., et al.
Publicado: (2023)

Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation
por: Matsunaga, Yasuhiro, et al.
Publicado: (2022)

Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline
por: Lau, Edmond Y., et al.
Publicado: (2021)

Non-Perturbative QCD Calculations of High-Energy Observables
por: Dosch, H G, et al.
Publicado: (1994)

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

Expression and Association of the Yersinia pestis Translocon Proteins, YopB and YopD, Are Facilitated by Nanolipoprotein Particles
por: Coleman, Matthew A., et al.
Publicado: (2016)

Computer programs for analytical perturbative calculations in high energy physics
por: Surguladze, L R
Publicado: (1994)

On the Improvement of Free-Energy Calculation from Steered Molecular Dynamics Simulations Using Adaptive Stochastic Perturbation Protocols
por: Perišić, Ognjen, et al.
Publicado: (2014)

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations
por: Conti, Simone, et al.
Publicado: (2022)

Re-directing bacterial microcompartment systems to enhance recombinant expression of lysis protein E from bacteriophage ϕX174 in Escherichia coli
por: Yung, Mimi C., et al.
Publicado: (2017)

Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity
por: Sergeeva, Alina P., et al.
Publicado: (2023)

Free energy perturbation (FEP)-guided scaffold hopping
por: Wu, Deyan, et al.
Publicado: (2022)

Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies
por: Fratev, Filip, et al.
Publicado: (2018)

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

Recent Calculations in Chiral Perturbation Theory
por: Gasser, J
Publicado: (2004)

Calculation of the Free Energy and Cooperativity of Protein Folding
por: Kentsis, Alex, et al.
Publicado: (2007)

Saturation Mutagenesis by Efficient Free-Energy Calculation
por: Jandova, Zuzana, et al.
Publicado: (2017)

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

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

Variational calculations with improved energy functionals in gauge theories
por: Heinemann, C., et al.
Publicado: (1999)

Calculating free energies of organic molecules on insulating substrates
por: Gaberle, Julian, et al.
Publicado: (2017)

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

On high-order perturbative calculations at finite density
por: Ghisoiu, Ioan, et al.
Publicado: (2016)

On gauge invariance and perturbative calculations in quantum chromodynamics
por: Curci, G, et al.
Publicado: (1978)

A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation
por: Rowley, Christopher N., et al.
Publicado: (2013)

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations
por: Zhang, Chun-Hui, et al.
Publicado: (2021)

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

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

Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing
por: Jaing, Crystal J., et al.
Publicado: (2016)

Assessing the Perturbing Effects of Drugs on Lipid Bilayers Using Gramicidin Channel-Based In Silico and In Vitro Assays
por: Sun, Delin, et al.
Publicado: (2020)

Conformational Dynamics of a Ligand-Free Adenylate Kinase
por: Song, Hyun Deok, et al.
Publicado: (2013)

Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples
por: Kimbrel, Jeffrey, et al.
Publicado: (2022)

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

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

On the Possibility of Calculating Entropy, Free Energy, and Enthalpy of Vitreous Substances
por: Nemilov, Sergei V.
Publicado: (2018)

Comparison of the Padé approximation method to perturbative QCD calculations
por: Samuel, Mark A., et al.
Publicado: (1995)

Perturbative Calculations And The Top Quark (ambiguity, Quantum Chromodynamics)
por: Smith, M C
Publicado: (1998)

Perturbative calculability and infrared behaviour in QCD at high temperature
por: D'Hoker, E
Publicado: (1982)

Cannot write session to /tmp/vufind_sessions/sess_3d5bu8bl9dmrffekl5gp1q84td