(Q34651994)

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Structural and dynamical insights on HLA-DR2 complexes that confer susceptibility to multiple sclerosis in Sardinia: a molecular dynamics simulation study

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Europe PubMed Central

PubMed publication ID

3 August 2017

Structural and dynamical insights on HLA-DR2 complexes that confer susceptibility to multiple sclerosis in Sardinia: a molecular dynamics simulation study (English)

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

multiple sclerosis

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object named as

Amit Kumar

1

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object named as

Enrico Pieroni

5

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object named as

Eleonora Cocco

2

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Maria Giovanna Marrosu

object named as

Maria Giovanna Marrosu

4

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3

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Luigi Atzori

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Europe PubMed Central

PubMed publication ID

3 August 2017

language of work or name

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publication date

26 March 2013

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Europe PubMed Central

PubMed publication ID

3 August 2017

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Europe PubMed Central

PubMed publication ID

3 August 2017

8

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

3

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

e59711

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

copyright license

Creative Commons Attribution 4.0 International

26 March 2013

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April 2022 Public Data File from Crossref

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0 references

HLA-DRB1-DQB1 haplotypes confer susceptibility and resistance to multiple sclerosis in Sardinia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex

1 reference

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7 July 2018

Molecular mimicry as an inducing trigger for CNS autoimmune demyelinating disease

1 reference

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7 July 2018

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles.

1 reference

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7 July 2018

Conformational lability in the class II MHC 310 helix and adjacent extended strand dictate HLA-DM susceptibility and peptide exchange

1 reference

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7 July 2018

Disparate Degrees of Hypervariable Loop Flexibility Control T-Cell Receptor Cross-Reactivity, Specificity, and Binding Mechanism

1 reference

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7 July 2018

Loss of T Cell Antigen Recognition Arising from Changes in Peptide and Major Histocompatibility Complex Protein Flexibility: IMPLICATIONS FOR VACCINE DESIGN

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Multiple sclerosis: new insights in pathogenesis and novel therapeutics.

1 reference

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7 July 2018

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

1 reference

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1 reference

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Small molecule modulators of MHC class II antigen presentation: mechanistic insights and implications for therapeutic application

1 reference

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Characterization of structural features controlling the receptiveness of empty class II MHC molecules.

1 reference

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7 July 2018

Environmental triggers of multiple sclerosis.

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Electrostatic modifications of the human leukocyte antigen-DR P9 peptide-binding pocket and susceptibility to primary sclerosing cholangitis

1 reference

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T cell receptor recognition of self and foreign antigens in the induction of autoimmunity

1 reference

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7 July 2018

Bidirectional binding of invariant chain peptides to an MHC class II molecule

1 reference

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A comparative approach linking molecular dynamics of altered peptide ligands and MHC with in vivo immune responses

1 reference

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7 July 2018

The role of antigen presenting cells in multiple sclerosis

1 reference

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7 July 2018

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

1 reference

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7 July 2018

Conformational heterogeneity of MHC class II induced upon binding to different peptides is a key regulator in antigen presentation and epitope selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

T Cell Receptor Cross-reactivity Directed by Antigen-Dependent Tuning of Peptide-MHC Molecular Flexibility

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Peptide binding to MHC class I and II proteins: new avenues from new methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

The binding of antigenic peptides to HLA-DR is influenced by interactions between pocket 6 and pocket 9.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

From genes to function: the next challenge to understanding multiple sclerosis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

T cell-mediated autoimmune disease due to low-affinity crossreactivity to common microbial peptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Variations in the electrostatic landscape of class II human leukocyte antigen molecule induced by modifications in the myelin basic protein peptide: a theoretical approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Model for the peptide-free conformation of class II MHC proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

The genetics of multiple sclerosis: SNPs to pathways to pathogenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

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Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex

1 reference

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A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach

1 reference

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7 July 2018

Anchor side chains of short peptide fragments trigger ligand-exchange of class II MHC molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Extraordinary cross-reactivity of an autoimmune T-cell receptor recognizing specific peptides both on autologous and on allogeneic HLA class II molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes

1 reference

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7 July 2018

Quantitative theories of T-cell responsiveness

1 reference

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7 July 2018

How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides?

1 reference

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7 July 2018

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.

1 reference

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The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

1 reference

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T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB.

1 reference

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7 July 2018

Scalable molecular dynamics with NAMD

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

MHCPred: A server for quantitative prediction of peptide-MHC binding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Development and current status of the CHARMM force field for nucleic acids.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Crystal structure of HLA-DR2 (DRA*0101, DRB1*1501) complexed with a peptide from human myelin basic protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

A new categorization of HLA DR alleles on a functional basis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Several common HLA-DR types share largely overlapping peptide binding repertoires

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

The class II MHC protein HLA-DR1 in complex with an endogenous peptide: implications for the structural basis of the specificity of peptide binding

1 reference

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7 July 2018

VMD: visual molecular dynamics

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Promiscuous and allele-specific anchors in HLA-DR-binding peptides

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7 July 2018

Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1.

1 reference

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7 July 2018

Comparative protein modelling by satisfaction of spatial restraints

1 reference

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7 July 2018

Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

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1 reference

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7 July 2018

The three-dimensional structure of peptide-MHC complexes

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The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

7 July 2018

Interactions between immunogenic peptides and MHC proteins

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3608583

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Extensive T cell receptor cross-reactivity on structurally diverse haptenated peptides presented by HLA-A2.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059711

21 January 2018

Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications.

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059711

21 January 2018

Heterogeneity at the HLA-DRB1 locus and risk for multiple sclerosis

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059711

21 January 2018

Epstein-Barr virus nuclear antigen-1 B-cell epitopes in multiple sclerosis twins.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059711

21 January 2018

Molecular simulations reveal the mechanism and the determinants for ampicillin translocation through OmpF.

1 reference

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21 January 2018

Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: a molecular dynamics simulation study

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059711

21 January 2018

PROCHECK: a program to check the stereochemical quality of protein structures

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21 January 2018

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21 January 2018

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

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21 January 2018

Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

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21 January 2018

Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins.

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21 January 2018

Viruses and multiple sclerosis

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26 October 2018

Altered peptide ligands of myelin basic protein ( MBP87-99 ) conjugated to reduced mannan modulate immune responses in mice

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https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0059711

21 January 2018

Multiple sclerosis associated amino acids of polymorphic regions relevant for the HLA antigen binding are confined to HLA-DR2

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21 January 2018

Analysis of key parameters for molecular dynamics of pMHC molecules

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21 January 2018

Conditional linkage disequilibrium analysis of a complex disease superlocus, IDDM1 in the HLA region, reveals the presence of independent modifying gene effects influencing the type 1 diabetes risk encoded by the major HLA-DQB1, -DRB1 disease loci

1 reference

https://pubmed.ncbi.nlm.nih.gov/23555757

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Immunology of multiple sclerosis

1 reference

https://pubmed.ncbi.nlm.nih.gov/23555757

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Software news and updates. Carma: a molecular dynamics analysis program

1 reference

https://pubmed.ncbi.nlm.nih.gov/23555757

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PONE.0059711

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

2013PLoSO...859711K

0 references

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

3 August 2017

ResearchGate publication ID

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