Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations (Q41874342)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23396076%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

title

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations (English)

1 reference

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23 February 2020

4

1 reference

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23 February 2020

8

Ken A Dill

1 reference

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23 February 2020

6

Bruce Kabakoff

1 reference

23 February 2020

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7

Thomas W Patapoff

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23 February 2020

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5

Ilya Chorny

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23 February 2020

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author name string

Ekaterine Kortkhonjia

1

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23 February 2020

Relly Brandman

2

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23 February 2020

Joe Zhongxiang Zhou

3

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23 February 2020

Trevor E Swartz

9

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23 February 2020

publication date

8 February 2013

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23 February 2020

published in

Monoclonal Antibodies

1 reference

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23 February 2020

volume

5

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23 February 2020

issue

2

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23 February 2020

page(s)

306-322

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

23 February 2020

cites work

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Perturbed heme binding is responsible for the blistering phenotype associated with mutations in the Caenorhabditis elegans dual oxidase 1 (DUOX1) peroxidase domain

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Construction, MD Simulation, and Hydrodynamic Validation of an All-Atom Model of a Monoclonal IgG Antibody

5 June 2018

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Everything you wanted to know about Markov State Models but were afraid to ask

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Protein folded states are kinetic hubs

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Structure and function of immunoglobulins

5 June 2018

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Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

5 June 2018

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Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

5 June 2018

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Progress and challenges in the automated construction of Markov state models for full protein systems

5 June 2018

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Design of therapeutic proteins with enhanced stability.

5 June 2018

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Site-specific conjugation of a cytotoxic drug to an antibody improves the therapeutic index.

5 June 2018

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Very fast prediction and rationalization of pKa values for protein-ligand complexes

5 June 2018

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Transition networks for modeling the kinetics of conformational change in macromolecules

5 June 2018

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Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

5 June 2018

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A consensus view of protein dynamics

5 June 2018

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Canonical sampling through velocity rescaling

5 June 2018

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oGNM: online computation of structural dynamics using the Gaussian Network Model

5 June 2018

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Automatic atom type and bond type perception in molecular mechanical calculations

5 June 2018

1 reference

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Very fast empirical prediction and rationalization of protein pKa values

5 June 2018

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iGNM: a database of protein functional motions based on Gaussian Network Model.

5 June 2018

1 reference

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Dynamics of antibodies from cryo-electron tomography

5 June 2018

1 reference

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Physical methods for structure, dynamics and binding in immunological research.

5 June 2018

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Structure, dynamics, and catalytic function of dihydrofolate reductase

5 June 2018

1 reference

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Development and testing of a general amber force field

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Freezing immunoglobulins to see them move

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Structure and flexibility of individual immunoglobulin G molecules in solution.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

The role of dynamics in enzyme activity

5 June 2018

1 reference

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Slaving: solvent fluctuations dominate protein dynamics and functions

5 June 2018

1 reference

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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

5 June 2018

1 reference

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An improved OPLS-AA force field for carbohydrates

5 June 2018

1 reference

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Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design

5 June 2018

1 reference

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Anisotropy of fluctuation dynamics of proteins with an elastic network model

5 June 2018

1 reference

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Mapping of the C1q binding site on rituxan, a chimeric antibody with a human IgG1 Fc

5 June 2018

1 reference

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The thermal stability of immunoglobulin: unfolding and aggregation of a multi-domain protein

5 June 2018

1 reference

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Crystallographic structure of an intact IgG1 monoclonal antibody

5 June 2018

1 reference

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Standard conformations for the canonical structures of immunoglobulins

5 June 2018

1 reference

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Steady-state polarization from cylindrically symmetric fluorophores undergoing rapid restricted motion

5 June 2018

1 reference

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X-ray structures of the antigen-binding domains from three variants of humanized anti-p185HER2 antibody 4D5 and comparison with molecular modeling

5 June 2018

1 reference

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The immunoglobulin fold. Structural classification, sequence patterns and common core

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

The structural requirements for complement activation by IgG: does it hinge on the hinge?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Nuclear magnetic resonance study of antibodies: a multinuclear approach

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Fluorescence resonance energy transfer

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Segmental flexibility of immunoglobulin G antibody molecules in solution: a new interpretation.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Analysis of time-resolved fluorescence anisotropy decays

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Nanosecond fluorescence spectroscopy of macromolecules

5 June 2018

1 reference

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Segmental flexibility and complement fixation of genetically engineered chimeric human, rabbit and mouse antibodies

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Influence of the hinge region on complement activation, C1q binding, and segmental flexibility in chimeric human immunoglobulins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3893241

Conformational flexibility of the ErbB2 ectodomain and trastuzumab antibody complex as revealed by molecular dynamics and principal component analysis.

5 June 2018

1 reference

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Probing dynamic protein ensembles with atomic proximity measures.

18 August 2018

1 reference

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The shear viscosity of rigid water models.

18 August 2018

1 reference

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Probability distributions of molecular observables computed from Markov models.

18 August 2018

1 reference

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Aspartate isomerization in the complementarity-determining regions of two closely related monoclonal antibodies.

18 August 2018

1 reference

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Anisotropic network model: systematic evaluation and a new web interface.

18 August 2018

1 reference

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Error analysis and efficient sampling in Markovian state models for molecular dynamics.

18 August 2018

1 reference

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Simulation of fluorescence anisotropy experiments: probing protein dynamics

18 August 2018

1 reference

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Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor

18 August 2018

1 reference

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Electron microscopy of an antibody-hapten complex.

18 August 2018

1 reference

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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

18 August 2018

1 reference

https://api.crossref.org/works/10.4161%2FMABS.23651

Contrasting IgG Structures Reveal Extreme Asymmetry and Flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FMABS.23651

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FMABS.23651

A dynamical study of antibody–antigen encounter reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FMABS.23651

Molecular Mechanism of Formation of an Antigen–Antibody Complex

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FMABS.23651

Correlation between segmental flexibility and effector function of antibodies

21 January 2018

1 reference

https://api.crossref.org/works/10.4161%2FMABS.23651

Concerning the axial rotational flexibility of the Fab regions of immunoglobulin G

21 January 2018

1 reference

12 December 2020

Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues

1 reference

12 December 2020

Electron microscopic evidence for the axial rotation and inter-domain flexibility of the Fab regions of immunoglobulin G

1 reference

12 December 2020

The molecular chaperonin cpn60 displays local flexibility that is reduced after binding with an unfolded protein

1 reference

12 December 2020

Canonical structures for the hypervariable regions of immunoglobulins

1 reference

12 December 2020

Full correlation analysis of conformational protein dynamics

1 reference

12 December 2020

Dynamical structure of the hinge region of immunoglobulin G as studied by 13C nuclear magnetic resonance spectroscopy

1 reference

12 December 2020

The Immunoglobulin Fold

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12 December 2020

Identifiers

DOI

10.4161/MABS.23651

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23396076%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23396076%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

PubMed publication ID

23396076

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23396076%20AND%20SRC:MED&resulttype=core&format=json