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Items: 1 to 20 of 96

1.

Local vs global motions in protein folding.

Maisuradze GG, Liwo A, Senet P, Scheraga HA.

J Chem Theory Comput. 2013 Jul 9;9(7):2907-2921.

2.

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.

Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA.

J Phys Chem A. 2010 Apr 8;114(13):4471-85. doi: 10.1021/jp9117776.

3.

Principal component analysis for protein folding dynamics.

Maisuradze GG, Liwo A, Scheraga HA.

J Mol Biol. 2009 Jan 9;385(1):312-29. doi: 10.1016/j.jmb.2008.10.018. Epub 2008 Oct 15.

4.

Relation between free energy landscapes of proteins and dynamics.

Maisuradze GG, Liwo A, Scheraga HA.

J Chem Theory Comput. 2010 Feb 9;6(2):583-595.

5.

How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?

Maisuradze GG, Liwo A, Scheraga HA.

Phys Rev Lett. 2009 Jun 12;102(23):238102. Epub 2009 Jun 12.

6.

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

Zhou R, Maisuradze GG, Suñol D, Todorovski T, Macias MJ, Xiao Y, Scheraga HA, Czaplewski C, Liwo A.

Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):18243-8. doi: 10.1073/pnas.1420914111. Epub 2014 Dec 8.

7.

Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain.

Maisuradze GG, Zhou R, Liwo A, Xiao Y, Scheraga HA.

J Mol Biol. 2012 Jul 20;420(4-5):350-65. doi: 10.1016/j.jmb.2012.04.027. Epub 2012 May 2.

8.

Preventing fibril formation of a protein by selective mutation.

Maisuradze GG, Medina J, Kachlishvili K, Krupa P, Mozolewska MA, Martin-Malpartida P, Maisuradze L, Macias MJ, Scheraga HA.

Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13549-54. doi: 10.1073/pnas.1518298112. Epub 2015 Oct 19.

9.

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains.

Liwo A, Khalili M, Scheraga HA.

Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2362-7. Epub 2005 Jan 26.

10.
11.

The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential.

Xu J, Huang L, Shakhnovich EI.

Proteins. 2011 Jun;79(6):1704-14. doi: 10.1002/prot.22993. Epub 2011 Mar 1.

12.

Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.

Lipska AG, Seidman SR, Sieradzan AK, Giełdoń A, Liwo A, Scheraga HA.

J Chem Phys. 2016 May 14;144(18):184110. doi: 10.1063/1.4948710.

13.

Free energy landscape of the FBP28 WW domain by all-atom direct folding simulation.

Kim E, Jang S, Lim M, Pak Y.

J Phys Chem B. 2010 Jun 10;114(22):7686-91. doi: 10.1021/jp102215j.

PMID:
20465282
15.

Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field.

Sieradzan AK, Niadzvedtski A, Scheraga HA, Liwo A.

J Chem Theory Comput. 2014 May 13;10(5):2194-2203. Epub 2014 Apr 15.

17.
18.

Folding dynamics of proteins from denatured to native state: principal component analysis.

Palazoglu A, Gursoy A, Arkun Y, Erman B.

J Comput Biol. 2004;11(6):1149-68.

PMID:
15662203
19.

Hidden protein folding pathways in free-energy landscapes uncovered by network analysis.

Yin Y, Maisuradze GG, Liwo A, Scheraga HA.

J Chem Theory Comput. 2012 Apr 10;8(4):1176-1189. Epub 2012 Feb 24.

20.

Kinks, loops, and protein folding, with protein A as an example.

Krokhotin A, Liwo A, Maisuradze GG, Niemi AJ, Scheraga HA.

J Chem Phys. 2014 Jan 14;140(2):025101. doi: 10.1063/1.4855735.

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