Freed KF - Search Results

1

Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.

Baxa MC, Haddadian EJ, Jumper JM, Freed KF, Sosnick TR. Baxa MC, et al. Among authors: freed kf. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15396-401. doi: 10.1073/pnas.1407768111. Epub 2014 Oct 13. Proc Natl Acad Sci U S A. 2014. PMID: 25313044 Free PMC article.

2

Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles.

Baxa MC, Haddadian EJ, Jha AK, Freed KF, Sosnick TR. Baxa MC, et al. Among authors: freed kf. J Am Chem Soc. 2012 Sep 26;134(38):15929-36. doi: 10.1021/ja3064028. Epub 2012 Sep 14. J Am Chem Soc. 2012. PMID: 22928488 Free PMC article.

3

De novo prediction of protein folding pathways and structure using the principle of sequential stabilization.

Adhikari AN, Freed KF, Sosnick TR. Adhikari AN, et al. Among authors: freed kf. Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17442-7. doi: 10.1073/pnas.1209000109. Epub 2012 Oct 8. Proc Natl Acad Sci U S A. 2012. PMID: 23045636 Free PMC article.

4

Simplified protein models: predicting folding pathways and structure using amino acid sequences.

Adhikari AN, Freed KF, Sosnick TR. Adhikari AN, et al. Among authors: freed kf. Phys Rev Lett. 2013 Jul 12;111(2):028103. doi: 10.1103/PhysRevLett.111.028103. Epub 2013 Jul 11. Phys Rev Lett. 2013. PMID: 23889448 Free PMC article.

5

Benchmarking all-atom simulations using hydrogen exchange.

Skinner JJ, Yu W, Gichana EK, Baxa MC, Hinshaw JR, Freed KF, Sosnick TR. Skinner JJ, et al. Among authors: freed kf. Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15975-80. doi: 10.1073/pnas.1404213111. Epub 2014 Oct 27. Proc Natl Acad Sci U S A. 2014. PMID: 25349413 Free PMC article.

6

Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.

Baxa MC, Yu W, Adhikari AN, Ge L, Xia Z, Zhou R, Freed KF, Sosnick TR. Baxa MC, et al. Among authors: freed kf. Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8302-7. doi: 10.1073/pnas.1503613112. Epub 2015 Jun 22. Proc Natl Acad Sci U S A. 2015. PMID: 26100906 Free PMC article.

7

Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.

Yu W, Baxa MC, Gagnon I, Freed KF, Sosnick TR. Yu W, et al. Among authors: freed kf. Proc Natl Acad Sci U S A. 2016 Apr 26;113(17):4747-52. doi: 10.1073/pnas.1522500113. Epub 2016 Apr 13. Proc Natl Acad Sci U S A. 2016. PMID: 27078098 Free PMC article.

8

Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.

Jumper JM, Faruk NF, Freed KF, Sosnick TR. Jumper JM, et al. Among authors: freed kf. PLoS Comput Biol. 2018 Dec 27;14(12):e1006578. doi: 10.1371/journal.pcbi.1006578. eCollection 2018 Dec. PLoS Comput Biol. 2018. PMID: 30589834 Free PMC article.

9

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.

Jumper JM, Faruk NF, Freed KF, Sosnick TR. Jumper JM, et al. Among authors: freed kf. PLoS Comput Biol. 2018 Dec 27;14(12):e1006342. doi: 10.1371/journal.pcbi.1006342. eCollection 2018 Dec. PLoS Comput Biol. 2018. PMID: 30589846 Free PMC article.

10

Mimicking the folding pathway to improve homology-free protein structure prediction.

DeBartolo J, Colubri A, Jha AK, Fitzgerald JE, Freed KF, Sosnick TR. DeBartolo J, et al. Among authors: freed kf. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3734-9. doi: 10.1073/pnas.0811363106. Epub 2009 Feb 23. Proc Natl Acad Sci U S A. 2009. PMID: 19237560 Free PMC article.

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