(Q40640535)

22 September 2017

Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure (English)

1 reference

22 September 2017

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26259654%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Valérie Gabelica

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26259654%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Frédéric Rosu

series ordinal

3

1 reference

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31 May 2020

author name string

Massimiliano Porrini

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26259654%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

language of work or name

1 reference

1 May 2015

1 reference

Journal of Mass Spectrometry

22 September 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26259654%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

volume

50

1 reference

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31 May 2020

issue

5

1 reference

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31 May 2020

page(s)

711-726

1 reference

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PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

31 May 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Ion mobility spectrometry: A personal view of its development at UCSB

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

All-atom empirical potential for molecular modeling and dynamics studies of proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

High resolution trapped ion mobility spectrometery of peptides

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

A theoretical view of protein dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Conformational ordering of biomolecules in the gas phase: nitrogen collision cross sections measured on a prototype high resolution drift tube ion mobility-mass spectrometer.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Ammonium ion binding to DNA G-quadruplexes: do electrospray mass spectra faithfully reflect the solution-phase species?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

UV spectroscopy of DNA duplex and quadruplex structures in the gas phase

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

How useful is ion mobility mass spectrometry for structural biology? The relationship between protein crystal structures and their collision cross sections in the gas phase

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Integrating ion mobility mass spectrometry with molecular modelling to determine the architecture of multiprotein complexes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Amyloid-β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Biomolecule analysis by ion mobility spectrometry

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Conformation of polyalanine and polyglycine dications in the gas phase: insight from ion mobility spectrometry and replica-exchange molecular dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Structural characterization of unsaturated phosphatidylcholines using traveling wave ion mobility spectrometry

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Ion mobility-mass spectrometry

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Structural and thermodynamic studies of the interaction of distamycin A with the parallel quadruplex structure [d(TGGGGT)]4

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Optimization by Simulated Annealing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

The dynamics of water evaporation from partially solvated cytochrome c in the gas phase.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Observation of the coexistence of sodium and calcium ions in a DNA G-quadruplex ion channel

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

The role of mass spectrometry in structure elucidation of dynamic protein complexes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Protein structures under electrospray conditions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Evidence for macromolecular protein rings in the absence of bulk water.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

The structure of gas-phase bradykinin fragment 1-5 (RPPGF) ions: an ion mobility spectrometry and H/D exchange ion-molecule reaction chemistry study

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Applications of a travelling wave-based radio-frequency-only stacked ring ion guide

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Investigation of intact protein complexes by mass spectrometry.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

The crystal structure of a parallel-stranded guanine tetraplex at 0.95 A resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

VMD: visual molecular dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Effective ion mobility calculations for macromolecules by scattering on electron clouds.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Collision cross sections of proteins and their complexes: a calibration framework and database for gas-phase structural biology

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Optimization of parameters used in algorithms of ion-mobility calculation for conformational analyses

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Fundamentals of traveling wave ion mobility spectrometry

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Early structural evolution of native cytochrome c after solvent removal.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Amyloid beta-protein monomer structure: a computational and experimental study.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

HyperChem: a software package for computational chemistry and molecular modeling.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

A mass-spectrometry-based framework to define the extent of disorder in proteins

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Dissecting the dynamic conformations of the metamorphic protein lymphotactin

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Fluorometric measurement and modeling of droplet temperature changes in an electrospray plume

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Factors contributing to the collision cross section of polyatomic ions in the kilodalton to gigadalton range: application to ion mobility measurements

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Statistical analysis of ion mobility spectrometry. II. Adaptively biased methods and shape correlations.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Structure of triplex DNA in the gas phase.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Structural characterization of drug-like compounds by ion mobility mass spectrometry: comparison of theoretical and experimentally derived nitrogen collision cross sections

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Statistical analysis of ion mobility spectrometry. I. Unbiased and guided replica-exchange molecular dynamics.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Folding of a salivary intrinsically disordered protein upon binding to tannins

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

On the structure elucidation using ion mobility spectrometry and molecular dynamics

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

G-quadruplex DNA assemblies: loop length, cation identity, and multimer formation

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Experimental and theoretical investigation into the correlation between mass and ion mobility for choline and other ammonium cations in N2.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Dynamics of B-DNA on the microsecond time scale.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Optimization of algorithms for ion mobility calculations.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

G-quadruplexes can maintain their structure in the gas phase.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4440389

Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last?

20 August 2018

1 reference

Electrospray ionization of large multiply charged species proceeds via Dole’s charged residue mechanism

21 January 2018

1 reference

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

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

21 January 2018

1 reference

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations

21 January 2018

1 reference

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Dynamics of Intact Immunoglobulin G Explored by Drift-Tube Ion-Mobility Mass Spectrometry and Molecular Modeling

21 January 2018

1 reference

A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (II). Model parameterization and definition of empirical shape factors for proteins

21 January 2018

1 reference

Stabilization and Structure of Telomeric and c-myc Region Intramolecular G-Quadruplexes: The Role of Central Cations and Small Planar Ligands

21 January 2018

1 reference

Ion mobility–mass spectrometry analysis of large protein complexes

21 January 2018

1 reference

12 December 2020

Traveling-wave ion mobility mass spectrometry of protein complexes: accurate calibrated collision cross-sections of human insulin oligomers

1 reference

12 December 2020

Charge-State Dependent Compaction and Dissociation of Protein Complexes: Insights from Ion Mobility and Molecular Dynamics

1 reference

12 December 2020

Infrared Signature of DNA G-Quadruplexes in the Gas Phase

1 reference

12 December 2020

The Structure and Dynamics of DNA in the Gas Phase

1 reference

12 December 2020

Mass spectrometry and ion mobility spectrometry of G-quadruplexes. A study of solvent effects on dimer formation and structural transitions in the telomeric DNA sequence d(TAGGGTTAGGGT)

1 reference

12 December 2020

Effective Temperature of Ions in Traveling Wave Ion Mobility Spectrometry

1 reference

12 December 2020

Identifiers

DOI

10.1002/JMS.3590

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26259654%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26259654%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26259654%20AND%20SRC:MED&resulttype=core&format=json