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For: Santini S, Mousseau N, Derreumaux P. In silico assembly of Alzheimer's Abeta16-22 peptide into beta-sheets. J Am Chem Soc 2004;126:11509-16. [PMID: 15366896 DOI: 10.1021/ja047286i] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Number Cited by Other Article(s)
1
Wang Z, Zhao C, Li Y, Wang J, Hou D, Wang L, Wang Y, Wang X, Liu X, Wang H, Xu W. Photostable Cascade-Activatable Peptide Self-Assembly on a Cancer Cell Membrane for High-Performance Identification of Human Bladder Cancer. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023;35:e2210732. [PMID: 37172955 DOI: 10.1002/adma.202210732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/10/2023] [Indexed: 05/15/2023]
2
Nguyen PH, Derreumaux P. Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations. J Chem Phys 2023;158:235101. [PMID: 37318171 DOI: 10.1063/5.0149419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023]  Open
3
Nguyen PH, Sterpone F, Derreumaux P. Metastable alpha-rich and beta-rich conformations of small Aβ42 peptide oligomers. Proteins 2023. [PMID: 37038252 DOI: 10.1002/prot.26495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023]
4
Nedaei H, Rezaei-Ghaleh N, Giller K, Becker S, Karami L, Moosavi-Movahedi AA, Griesinger C, Saboury AA. The Calcium-free form of Atorvastatin inhibits amyloid-β(1-42) aggregation in vitro. J Biol Chem 2022;298:101662. [PMID: 35104501 PMCID: PMC8898965 DOI: 10.1016/j.jbc.2022.101662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 11/29/2022]  Open
5
Nguyen PH, Derreumaux P. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation. Methods Mol Biol 2022;2340:175-196. [PMID: 35167075 DOI: 10.1007/978-1-0716-1546-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
6
Nguyen PH, Tufféry P, Derreumaux P. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations. Methods Mol Biol 2022;2405:95-113. [PMID: 35298810 DOI: 10.1007/978-1-0716-1855-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
7
An H, Mamuti M, Wang X, Yao H, Wang M, Zhao L, Li L. Rationally designed modular drug delivery platform based on intracellular peptide self‐assembly. EXPLORATION 2021;1:20210153. [PMCID: PMC10190849 DOI: 10.1002/exp.20210153] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/08/2021] [Indexed: 06/14/2023]
8
Sahoo A, Matysiak S. Effects of applied surface-tension on membrane-assisted Aβ aggregation. Phys Chem Chem Phys 2021;23:20627-20633. [PMID: 34514475 DOI: 10.1039/d1cp02642a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
9
Illig AM, Strodel B. Performance of Markov State Models and Transition Networks on Characterizing Amyloid Aggregation Pathways from MD Data. J Chem Theory Comput 2020;16:7825-7839. [DOI: 10.1021/acs.jctc.0c00727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
10
Samantray S, Yin F, Kav B, Strodel B. Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations. J Chem Inf Model 2020;60:6462-6475. [DOI: 10.1021/acs.jcim.0c01063] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
11
Xiao WY, Wang Y, An HW, Hou D, Mamuti M, Wang MD, Wang J, Xu W, Hu L, Wang H. Click Reaction-Assisted Peptide Immune Checkpoint Blockade for Solid Tumor Treatment. ACS APPLIED MATERIALS & INTERFACES 2020;12:40042-40051. [PMID: 32805827 DOI: 10.1021/acsami.0c10166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
12
Theoretical and computational advances in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020;118:1-31. [PMID: 31928722 DOI: 10.1016/bs.apcsb.2019.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
13
Nguyen PH, Sterpone F, Derreumaux P. Aggregation of disease-related peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020;170:435-460. [PMID: 32145950 DOI: 10.1016/bs.pmbts.2019.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
14
A tumour-selective cascade activatable self-detained system for drug delivery and cancer imaging. Nat Commun 2019;10:4861. [PMID: 31649241 PMCID: PMC6813295 DOI: 10.1038/s41467-019-12848-5] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]  Open
15
Wang Z, An HW, Hou D, Wang M, Zeng X, Zheng R, Wang L, Wang K, Wang H, Xu W. Addressable Peptide Self-Assembly on the Cancer Cell Membrane for Sensitizing Chemotherapy of Renal Cell Carcinoma. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019;31:e1807175. [PMID: 30663139 DOI: 10.1002/adma.201807175] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/02/2019] [Indexed: 05/06/2023]
16
Man VH, He X, Derreumaux P, Ji B, Xie XQ, Nguyen PH, Wang J. Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16-22 Dimer. J Chem Theory Comput 2019;15:1440-1452. [PMID: 30633867 PMCID: PMC6745714 DOI: 10.1021/acs.jctc.8b01107] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
17
Li X, Lei J, Qi R, Xie L, Wei G. Mechanistic insight into E22Q-mutation-induced antiparallel-to-parallel β-sheet transition of Aβ16−22fibrils: an all-atom simulation study. Phys Chem Chem Phys 2019;21:15686-15694. [DOI: 10.1039/c9cp02561h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
18
Sahoo A, Xu H, Matysiak S. Pathways of amyloid-beta absorption and aggregation in a membranous environment. Phys Chem Chem Phys 2019;21:8559-8568. [PMID: 30964132 DOI: 10.1039/c9cp00040b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
19
Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018;118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
20
Rodriguez RA, Chen LY, Plascencia-Villa G, Perry G. Thermodynamics of Amyloid-β Fibril Elongation: Atomistic Details of the Transition State. ACS Chem Neurosci 2018;9:783-789. [PMID: 29239603 PMCID: PMC5911799 DOI: 10.1021/acschemneuro.7b00409] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
21
Sun Y, Wang B, Ge X, Ding F. Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide. Phys Chem Chem Phys 2017;19:28414-28423. [PMID: 29038815 PMCID: PMC5657190 DOI: 10.1039/c7cp05695h] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
22
Rengifo RF, Li NX, Sementilli A, Lynn DG. Amyloid scaffolds as alternative chlorosomes. Org Biomol Chem 2017;15:7063-7071. [PMID: 28715014 PMCID: PMC5577367 DOI: 10.1039/c7ob01170a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
23
Dorosh L, Stepanova M. Probing oligomerization of amyloid beta peptide in silico. MOLECULAR BIOSYSTEMS 2017;13:165-182. [PMID: 27844078 DOI: 10.1039/c6mb00441e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
24
Tran TT, Nguyen PH, Derreumaux P. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides. J Chem Phys 2017;144:205103. [PMID: 27250331 DOI: 10.1063/1.4951739] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
25
Chiricotto M, Tran TT, Nguyen PH, Melchionna S, Sterpone F, Derreumaux P. Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
26
Schwierz N, Frost CV, Geissler PL, Zacharias M. Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step. J Am Chem Soc 2016;138:527-39. [PMID: 26694883 DOI: 10.1021/jacs.5b08717] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
27
Martinez AV, Małolepsza E, Rivera E, Lu Q, Straub JE. Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles. J Chem Phys 2015;141:22D530. [PMID: 25494801 DOI: 10.1063/1.4902550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
28
Zhang T, Nguyen PH, Nasica-Labouze J, Mu Y, Derreumaux P. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J Phys Chem B 2015;119:6941-51. [PMID: 25985144 DOI: 10.1021/acs.jpcb.5b03381] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
29
Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015;115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 474] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
30
Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015;115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
31
Liang C, Ni R, Smith JE, Childers WS, Mehta AK, Lynn DG. Kinetic Intermediates in Amyloid Assembly. J Am Chem Soc 2014;136:15146-9. [DOI: 10.1021/ja508621b] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
32
Tsigelny IF, Sharikov Y, Kouznetsova VL, Greenberg JP, Wrasidlo W, Gonzalez T, Desplats P, Michael SE, Trejo-Morales M, Overk CR, Masliah E. Structural diversity of Alzheimer's disease amyloid-β dimers and their role in oligomerization and fibril formation. J Alzheimers Dis 2014;39:583-600. [PMID: 24240640 DOI: 10.3233/jad-131589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
33
Han W, Schulten K. Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations. J Am Chem Soc 2014;136:12450-60. [PMID: 25134066 PMCID: PMC4156860 DOI: 10.1021/ja507002p] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
34
Xu L, Chen Y, Wang X. Assembly of Amyloid β Peptides in the Presence of Fibril Seeds: One-Pot Coarse-Grained Molecular Dynamics Simulations. J Phys Chem B 2014;118:9238-46. [DOI: 10.1021/jp505551m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
35
Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014;43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
36
Lin D, Luo Y, Wu S, Ma Q, Wei G, Yang X. Investigation of the aggregation process of amyloid-β-(16-22) peptides and the dissolution of intermediate aggregates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014;30:3170-3175. [PMID: 24588450 DOI: 10.1021/la4048165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
37
Ning L, Guo J, Bai Q, Jin N, Liu H, Yao X. Structural diversity and initial oligomerization of PrP106-126 studied by replica-exchange and conventional molecular dynamics simulations. PLoS One 2014;9:e87266. [PMID: 24586266 PMCID: PMC3929351 DOI: 10.1371/journal.pone.0087266] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/24/2013] [Indexed: 12/15/2022]  Open
38
Nguyen P, Derreumaux P. Understanding amyloid fibril nucleation and aβ oligomer/drug interactions from computer simulations. Acc Chem Res 2014;47:603-11. [PMID: 24368046 DOI: 10.1021/ar4002075] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
39
Liu J, Wang W, Zhang Q, Zhang S, Yuan Z. Study on the Efficiency and Interaction Mechanism of a Decapeptide Inhibitor of β-Amyloid Aggregation. Biomacromolecules 2014;15:931-9. [DOI: 10.1021/bm401795e] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
40
Gill AC. β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides. PLoS One 2014;9:e87354. [PMID: 24498083 PMCID: PMC3909104 DOI: 10.1371/journal.pone.0087354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/19/2013] [Indexed: 01/09/2023]  Open
41
Nguyen PH, Tarus B, Derreumaux P. Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1–28 Monomer. J Phys Chem B 2014;118:501-10. [DOI: 10.1021/jp4115404] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
42
Spiga E, Degiacomi MT, Dal Peraro M. New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014;96:77-111. [DOI: 10.1016/bs.apcsb.2014.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
43
Nguyen PH, Derreumaux P. Conformational ensemble and polymorphism of the all-atom Alzheimer's Aβ(37-42) amyloid peptide oligomers. J Phys Chem B 2013;117:5831-40. [PMID: 23581814 DOI: 10.1021/jp401563n] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
44
Ni B, Baumketner A. Reduced atomic pair-interaction design (RAPID) model for simulations of proteins. J Chem Phys 2013;138:064102. [PMID: 23425456 PMCID: PMC3579890 DOI: 10.1063/1.4790160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 01/18/2013] [Indexed: 12/15/2022]  Open
45
Derreumaux P. Coarse-grained models for protein folding and aggregation. Methods Mol Biol 2013;924:585-600. [PMID: 23034764 DOI: 10.1007/978-1-62703-017-5_22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
46
Lu Y, Wei G, Derreumaux P. Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations. J Chem Phys 2012;137:025101. [PMID: 22803563 DOI: 10.1063/1.4732761] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
47
Chebaro Y, Pasquali S, Derreumaux P. The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins. J Phys Chem B 2012;116:8741-52. [DOI: 10.1021/jp301665f] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
48
Waldauer SA, Hassan S, Paoli B, Donaldson PM, Pfister R, Hamm P, Caflisch A, Pellarin R. Photocontrol of Reversible Amyloid Formation with a Minimal-Design Peptide. J Phys Chem B 2012;116:8961-73. [DOI: 10.1021/jp305311z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
49
Childers WS, Anthony NR, Mehta AK, Berland KM, Lynn DG. Phase networks of cross-β peptide assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012;28:6386-6395. [PMID: 22439620 DOI: 10.1021/la300143j] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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