Format
Sort by

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 115

1.

Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer's amyloid β-peptide.

Gerben SR, Lemkul JA, Brown AM, Bevan DR.

J Biomol Struct Dyn. 2014;32(11):1817-32. doi: 10.1080/07391102.2013.838518. Epub 2013 Sep 13.

PMID:
24028075
2.

The Dependence of Amyloid-β Dynamics on Protein Force Fields and Water Models.

Somavarapu AK, Kepp KP.

Chemphyschem. 2015 Oct 26;16(15):3278-89. doi: 10.1002/cphc.201500415. Epub 2015 Aug 19.

PMID:
26256268
3.

Secondary Structure of Rat and Human Amylin across Force Fields.

Hoffmann KQ, McGovern M, Chiu CC, de Pablo JJ.

PLoS One. 2015 Jul 29;10(7):e0134091. doi: 10.1371/journal.pone.0134091. eCollection 2015.

4.

Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ(16-22) dimer and trimer.

Nguyen PH, Li MS, Derreumaux P.

Phys Chem Chem Phys. 2011 May 28;13(20):9778-88. doi: 10.1039/c1cp20323a. Epub 2011 Apr 12.

PMID:
21487594
5.

Amyloid peptide Aβ40 inhibits aggregation of Aβ42: evidence from molecular dynamics simulations.

Viet MH, Li MS.

J Chem Phys. 2012 Jun 28;136(24):245105. doi: 10.1063/1.4730410.

PMID:
22755606
6.

Distinguishing amyloid fibril structures in Alzheimer's disease (AD) by two-dimensional ultraviolet (2DUV) spectroscopy.

Lam AR, Jiang J, Mukamel S.

Biochemistry. 2011 Nov 15;50(45):9809-16. doi: 10.1021/bi201317c. Epub 2011 Oct 20. Erratum in: Biochemistry. 2012 Aug 7;51(31):6262.

7.

Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment.

Kent A, Jha AK, Fitzgerald JE, Freed KF.

J Phys Chem B. 2008 May 15;112(19):6175-86. doi: 10.1021/jp077099h. Epub 2008 Mar 19.

8.

Dynamics of protofibril elongation and association involved in Aβ42 peptide aggregation in Alzheimer's disease.

Ghosh P, Kumar A, Datta B, Rangachari V.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S24. doi: 10.1186/1471-2105-11-S6-S24.

9.

Molecular mechanism of misfolding and aggregation of Aβ(13-23).

Lovas S, Zhang Y, Yu J, Lyubchenko YL.

J Phys Chem B. 2013 May 23;117(20):6175-86. doi: 10.1021/jp402938p. Epub 2013 May 15.

10.

Structures of the amyloid β-peptides Aβ1-40 and Aβ1-42 as influenced by pH and a D-peptide.

Olubiyi OO, Strodel B.

J Phys Chem B. 2012 Mar 15;116(10):3280-91. doi: 10.1021/jp2076337. Epub 2012 Mar 1.

PMID:
22300010
11.

Force-Field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields.

Smith MD, Rao JS, Segelken E, Cruz L.

J Chem Inf Model. 2015 Dec 28;55(12):2587-95. doi: 10.1021/acs.jcim.5b00308. Epub 2015 Dec 16.

PMID:
26629886
12.
13.

A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28)).

Rojas AV, Liwo A, Scheraga HA.

J Phys Chem B. 2011 Nov 10;115(44):12978-83. doi: 10.1021/jp2050993. Epub 2011 Oct 18.

14.

Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations.

Fawzi NL, Phillips AH, Ruscio JZ, Doucleff M, Wemmer DE, Head-Gordon T.

J Am Chem Soc. 2008 May 14;130(19):6145-58. doi: 10.1021/ja710366c. Epub 2008 Apr 16. Erratum in: J Am Chem Soc. 2011 Aug 3;133(30):11816.

15.

Polymorphic structures of Alzheimer's β-amyloid globulomers.

Yu X, Zheng J.

PLoS One. 2011;6(6):e20575. doi: 10.1371/journal.pone.0020575. Epub 2011 Jun 7.

16.

How the amyloid-β peptide and membranes affect each other: an extensive simulation study.

Poojari C, Kukol A, Strodel B.

Biochim Biophys Acta. 2013 Feb;1828(2):327-39. doi: 10.1016/j.bbamem.2012.09.001. Epub 2012 Sep 10.

17.

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations.

Cino EA, Choy WY, Karttunen M.

J Chem Theory Comput. 2012 Aug 14;8(8):2725-2740. Epub 2012 Jun 19.

18.

Three force fields' views of the 3(10) helix.

Patapati KK, Glykos NM.

Biophys J. 2011 Oct 5;101(7):1766-71. doi: 10.1016/j.bpj.2011.08.044.

19.

Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal.

Hu Z, Jiang J.

J Comput Chem. 2010 Jan 30;31(2):371-80. doi: 10.1002/jcc.21330.

PMID:
19479737
20.

Aggregation of Alzheimer's amyloid β-peptide in biological membranes: a molecular dynamics study.

Lemkul JA, Bevan DR.

Biochemistry. 2013 Jul 23;52(29):4971-80. doi: 10.1021/bi400562x. Epub 2013 Jul 15.

PMID:
23855340
Items per page

Supplemental Content

Write to the Help Desk