(Q38061633)

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The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease

scientific article published on 27 August 2012

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scholarly article

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Europe PubMed Central

PMC publication ID

28 August 2017

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Europe PubMed Central

The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease (English)

1 reference

Europe PubMed Central

PMC publication ID

28 August 2017

Alzheimer's disease

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author name string

Justin A Lemkul

1

1 reference

Europe PubMed Central

PMC publication ID

28 August 2017

David R Bevan

2

1 reference

Europe PubMed Central

PMC publication ID

28 August 2017

language of work or name

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based on heuristic

inferred from title

publication date

27 August 2012

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Europe PubMed Central

PMC publication ID

28 August 2017

ACS Chemical Neuroscience

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Europe PubMed Central

PMC publication ID

28 August 2017

3

1 reference

Europe PubMed Central

PMC publication ID

28 August 2017

11

1 reference

Europe PubMed Central

PMC publication ID

28 August 2017

845-856

1 reference

Europe PubMed Central

PMC publication ID

28 August 2017

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

1 reference

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Comparison of three amyloid assembly inhibitors: the sugar scyllo-inositol, the polyphenol epigallocatechin gallate, and the molecular tweezer CLR01

1 reference

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Design of β-amyloid aggregation inhibitors from a predicted structural motif

1 reference

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Phenolic compounds prevent amyloid β-protein oligomerization and synaptic dysfunction by site-specific binding

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Structures of Aβ17-42 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure

1 reference

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Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets

1 reference

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Pharmacotherapies for Alzheimer's disease: beyond cholinesterase inhibitors

1 reference

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Disordered binding of small molecules to Aβ(12-28).

1 reference

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1 reference

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Lipid composition influences the release of Alzheimer's amyloid β-peptide from membranes.

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Structural basis for Aβ1–42 toxicity inhibition by Aβ C-terminal fragments: discrete molecular dynamics study.

1 reference

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Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms

1 reference

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Nonsteroidal anti-inflammatory drug naproxen destabilizes Aβ amyloid fibrils: a molecular dynamics investigation.

1 reference

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Characterizing amyloid‐beta protein misfolding from molecular dynamics simulations with explicit water

1 reference

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Binding of nonsteroidal anti-inflammatory drugs to Abeta fibril

1 reference

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1 reference

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Molecular dynamics simulations of anti-aggregation effect of ibuprofen.

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Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase

1 reference

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6 September 2017

Molecular dynamics simulations of Ibuprofen binding to Abeta peptides

1 reference

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Computational selection of inhibitors of Abeta aggregation and neuronal toxicity.

1 reference

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Interaction between amyloid-beta (1-42) peptide and phospholipid bilayers: a molecular dynamics study

1 reference

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Amyloid beta-protein assembly as a therapeutic target of Alzheimer's disease

1 reference

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Molecular structural basis for polymorphism in Alzheimer's -amyloid fibrils

1 reference

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The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulations

1 reference

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6 September 2017

Amyloid beta-protein assembly and Alzheimer disease

1 reference

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Amyloid beta-protein monomer folding: free-energy surfaces reveal alloform-specific differences

1 reference

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6 September 2017

Role of the region 23-28 in Abeta fibril formation: insights from simulations of the monomers and dimers of Alzheimer's peptides Abeta40 and Abeta42.

1 reference

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Additive empirical force field for hexopyranose monosaccharides

1 reference

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Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

1 reference

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1 reference

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New insights into the mechanism of Alzheimer amyloid-beta fibrillogenesis inhibition by N-methylated peptides

1 reference

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1 reference

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6 September 2017

The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study

1 reference

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Methodology for multi-site ligand-protein docking identification developed for the optimization of spirostenol inhibition of beta-amyloid-induced neurotoxicity

1 reference

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6 September 2017

Computer simulations of Alzheimer's amyloid beta-protein folding and assembly

1 reference

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1 reference

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Elucidating amyloid beta-protein folding and assembly: A multidisciplinary approach

1 reference

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

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Spatial separation of beta-sheet domains of beta-amyloid: disruption of each beta-sheet by N-methyl amino acids

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Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils

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3D structure of Alzheimer's amyloid-beta(1-42) fibrils

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Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments

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Design of peptidyl compounds that affect beta-amyloid aggregation: importance of surface tension and context

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Conformational transition of amyloid beta-peptide

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Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis

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6 September 2017

Amyloid fibers are water-filled nanotubes

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6 September 2017

The Alzheimer's peptide a beta adopts a collapsed coil structure in water

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6 September 2017

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Structure of amyloid A4-(1-40)-peptide of Alzheimer's disease

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6 September 2017

Molecular dynamics simulations in biology

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6 September 2017

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6 September 2017

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6 September 2017

Thermodynamics of ligand binding and efficiency

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6 September 2017

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14 September 2017

Molecular dynamics simulation of amyloid beta dimer formation

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14 September 2017

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14 September 2017

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28 September 2017

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23 June 2018

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23 June 2018

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23 June 2018

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23 June 2018

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23 June 2018

A coarse-grained protein force field for folding and structure prediction.

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23 June 2018

Pharmacological profiles of peptide drug candidates for the treatment of Alzheimer's disease

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23 June 2018

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

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31 August 2018

Morin inhibits the early stages of amyloid β-peptide aggregation by altering tertiary and quaternary interactions to produce "off-pathway" structures

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31 August 2018

Amyloid β peptides aggregation in a mixed membrane bilayer: a molecular dynamics study.

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31 August 2018

Effects of G33A and G33I mutations on the structures of monomer and dimer of the amyloid-β fragment 29-42 by replica exchange molecular dynamics simulations

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31 August 2018

Destabilizing Alzheimer's Abeta(42) protofibrils with morin: mechanistic insights from molecular dynamics simulations

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31 August 2018

Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study.

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Reconstruction of atomistic details from coarse-grained structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Assessing the stability of Alzheimer's amyloid protofibrils using molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Molecular insight into the inhibition effect of trehalose on the nucleation and elongation of amyloid beta-peptide oligomers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Perturbation of membranes by the amyloid beta-peptide--a molecular dynamics study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Structures and thermodynamics of Alzheimer's amyloid-beta Abeta(16-35) monomer and dimer by replica exchange molecular dynamics simulations: implication for full-length Abeta fibrillation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Targeting the early steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors: a numerical study.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

A comparative molecular dynamics analysis of the amyloid beta-peptide in a lipid bilayer.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Harnessing chaperones to generate small-molecule inhibitors of amyloid beta aggregation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Anti-amyloidogenic activity of tannic acid and its activity to destabilize Alzheimer's beta-amyloid fibrils in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Permeabilization of lipid bilayers is a common conformation-dependent activity of soluble amyloid oligomers in protein misfolding diseases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Curcumin has potent anti-amyloidogenic effects for Alzheimer's beta-amyloid fibrils in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Nicotine breaks down preformed Alzheimer's beta-amyloid fibrils in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Inhibition of beta-amyloid(40) fibrillogenesis and disassembly of beta-amyloid(40) fibrils by short beta-amyloid congeners containing N-methyl amino acids at alternate residues

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Structure-function relationships for inhibitors of beta-amyloid toxicity containing the recognition sequence KLVFF.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Simulations of protein folding and unfolding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

The alpha-helical to beta-strand transition in the amino-terminal fragment of the amyloid beta-peptide modulates amyloid formation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

31 August 2018

Docking Ligands on Protein Surfaces: The Case Study of Prion Protein

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

1 October 2018

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Capturing intermediate structures of Alzheimer's beta-amyloid, Abeta(1-40), by solid-state NMR spectroscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

1 October 2018

Distinct Morphologies for Amyloid Beta Protein Monomer: Aβ1–40, Aβ1–42, and Aβ1–40(D23N)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

3 December 2018

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

3 December 2018

Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: Aβ1–40, Aβ1–42, and Aβ1–40(D23N)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

3 December 2018

Rational Design of β-Sheet Ligands Against Aβ42-Induced Toxicity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

3 December 2018

Misfolding of the amyloid β-protein: A molecular dynamics study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3503341

3 December 2018

Characterizing the structural behavior of selected Aβ-42 monomers with different solubilities

1 reference

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

1 reference

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular insight into conformational transition of amyloid β-peptide 42 inhibited by (-)-epigallocatechin-3-gallate probed by molecular simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Inhibitor discovery targeting the intermediate structure of beta-amyloid peptide on the conformational transition pathway: implications in the aggregation mechanism of beta-amyloid peptide

1 reference

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Inhibition of aggregation of amyloid peptides by beta-sheet breaker peptides and their binding affinity

1 reference

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Arrest of beta-amyloid fibril formation by a pentapeptide ligand

1 reference

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A strategy for designing inhibitors of beta-amyloid toxicity

1 reference

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure of the amyloid-beta (1-42) monomer absorbed to model phospholipid bilayers: a molecular dynamics study

1 reference

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structures of the Amyloid β-Peptides Aβ1–40 and Aβ1–42 as Influenced by pH and a d-Peptide

1 reference

https://pubmed.ncbi.nlm.nih.gov/23173066

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/CN300091A

1 reference

Europe PubMed Central

PMC publication ID

28 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

28 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

28 August 2017

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