Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 115

1.

Dynamical phase transitions reveal amyloid-like states on protein folding landscapes.

Weber JK, Jack RL, Schwantes CR, Pande VS.

Biophys J. 2014 Aug 19;107(4):974-82. doi: 10.1016/j.bpj.2014.06.046.

2.

Markov state models provide insights into dynamic modulation of protein function.

Shukla D, Hernández CX, Weber JK, Pande VS.

Acc Chem Res. 2015 Feb 17;48(2):414-22. doi: 10.1021/ar5002999. Epub 2015 Jan 3. Review.

3.

Percolation-like phase transitions in network models of protein dynamics.

Weber JK, Pande VS.

J Chem Phys. 2015 Jun 7;142(21):215105. doi: 10.1063/1.4921989.

4.
5.

Efficient traversal of beta-sheet protein folding pathways using ensemble models.

Shenker S, O'Donnell CW, Devadas S, Berger B, Waldispühl J.

J Comput Biol. 2011 Nov;18(11):1635-47. doi: 10.1089/cmb.2011.0176. Epub 2011 Sep 29.

PMID:
21958108
6.

Role of water in protein aggregation and amyloid polymorphism.

Thirumalai D, Reddy G, Straub JE.

Acc Chem Res. 2012 Jan 17;45(1):83-92. doi: 10.1021/ar2000869. Epub 2011 Jul 15.

7.

Dominance of misfolded intermediates in the dynamics of α-helix folding.

Lin MM, Shorokhov D, Zewail AH.

Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14424-9. doi: 10.1073/pnas.1416300111. Epub 2014 Sep 22.

9.

Phosphorylation as conformational switch from the native to amyloid state: Trp-cage as a protein aggregation model.

Kardos J, Kiss B, Micsonai A, Rovó P, Menyhárd DK, Kovács J, Váradi G, Tóth GK, Perczel A.

J Phys Chem B. 2015 Feb 19;119(7):2946-55. doi: 10.1021/jp5124234. Epub 2015 Feb 6.

PMID:
25625571
10.

Emergence of glass-like behavior in Markov state models of protein folding dynamics.

Weber JK, Jack RL, Pande VS.

J Am Chem Soc. 2013 Apr 17;135(15):5501-4. doi: 10.1021/ja4002663. Epub 2013 Apr 3.

11.

Conformational propagation with prion-like characteristics in a simple model of protein folding.

Harrison PM, Chan HS, Prusiner SB, Cohen FE.

Protein Sci. 2001 Apr;10(4):819-35.

12.

Multiscale simulations of protein folding: application to formation of secondary structures.

Xu J, Ren Y, Li J.

J Biomol Struct Dyn. 2013;31(7):779-87. doi: 10.1080/07391102.2012.709461. Epub 2012 Aug 22.

PMID:
22908945
13.

Network approach to identify the folding transition states of peptides and proteins.

Jiang X, Zhong A, Chen C, Huang Y, Xiao Y.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Nov;86(5 Pt 1):051901. Epub 2012 Nov 2.

PMID:
23214808
14.

Protein folded states are kinetic hubs.

Bowman GR, Pande VS.

Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10890-5. doi: 10.1073/pnas.1003962107. Epub 2010 Jun 1. Erratum in: Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16749.

15.

Oligomerization of the human prion protein proceeds via a molten globule intermediate.

Gerber R, Tahiri-Alaoui A, Hore PJ, James W.

J Biol Chem. 2007 Mar 2;282(9):6300-7. Epub 2007 Jan 8.

16.

Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.

Schwantes CR, Shukla D, Pande VS.

Biophys J. 2016 Apr 26;110(8):1716-1719. doi: 10.1016/j.bpj.2016.03.026.

17.

A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models.

Husic BE, McKiernan KA, Wayment-Steele HK, Sultan MM, Pande VS.

J Chem Theory Comput. 2018 Feb 13;14(2):1071-1082. doi: 10.1021/acs.jctc.7b01004. Epub 2018 Jan 24.

PMID:
29253336
18.

Metastable, partially folded states in the productive folding and in the misfolding and amyloid aggregation of proteins.

Ferreira ST, De Felice FG, Chapeaurouge A.

Cell Biochem Biophys. 2006;44(3):539-48. Review.

PMID:
16679542
19.

Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing.

Lipfert J, Franklin J, Wu F, Doniach S.

J Mol Biol. 2005 Jun 10;349(3):648-58. Epub 2005 Apr 13.

PMID:
15896350
20.

Dynamics of noncovalent interactions in all-α and all-β class proteins: implications for the stability of amyloid aggregates.

Jain A, Sankararamakrishnan R.

J Chem Inf Model. 2011 Dec 27;51(12):3208-16. doi: 10.1021/ci200302q. Epub 2011 Nov 14.

PMID:
22017310

Supplemental Content

Support Center