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Results: 1 to 20 of 105

1.

Evolutionary optimization of protein folding.

Debès C, Wang M, Caetano-Anollés G, Gräter F.

PLoS Comput Biol. 2013;9(1):e1002861. doi: 10.1371/journal.pcbi.1002861. Epub 2013 Jan 17.

PMID:
23341762
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Factors governing the foldability of proteins.

Klimov DK, Thirumalai D.

Proteins. 1996 Dec;26(4):411-41.

PMID:
8990496
[PubMed - indexed for MEDLINE]
3.

Proteome evolution and the metabolic origins of translation and cellular life.

Caetano-Anollés D, Kim KM, Mittenthal JE, Caetano-Anollés G.

J Mol Evol. 2011 Jan;72(1):14-33. doi: 10.1007/s00239-010-9400-9. Epub 2010 Nov 17.

PMID:
21082171
[PubMed - indexed for MEDLINE]
4.
5.

The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.

Kim KM, Caetano-Anollés G.

BMC Evol Biol. 2012 Jan 27;12:13. doi: 10.1186/1471-2148-12-13.

PMID:
22284070
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Navigating the downhill protein folding regime via structural homologues.

Naganathan AN, Li P, Perez-Jimenez R, Sanchez-Ruiz JM, Muñoz V.

J Am Chem Soc. 2010 Aug 18;132(32):11183-90. doi: 10.1021/ja103612q.

PMID:
20698685
[PubMed - indexed for MEDLINE]
7.

Folding simulations of a de novo designed protein with a betaalphabeta fold.

Qi Y, Huang Y, Liang H, Liu Z, Lai L.

Biophys J. 2010 Jan 20;98(2):321-9. doi: 10.1016/j.bpj.2009.10.018.

PMID:
20338854
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Protein folding rates estimated from contact predictions.

Punta M, Rost B.

J Mol Biol. 2005 May 6;348(3):507-12.

PMID:
15826649
[PubMed - indexed for MEDLINE]
9.

Understanding the effect of secondary structures and aggregation on human protein folding class evolution.

Begum T, Ghosh TC.

J Mol Evol. 2010 Jul;71(1):60-9. doi: 10.1007/s00239-010-9364-9. Epub 2010 Jul 7.

PMID:
20614111
[PubMed - indexed for MEDLINE]
10.

Positive selection dictates the choice between kinetic and thermodynamic protein folding and stability in subtilases.

Subbian E, Yabuta Y, Shinde U.

Biochemistry. 2004 Nov 16;43(45):14348-60.

PMID:
15533039
[PubMed - indexed for MEDLINE]
11.

An evolutionarily structured universe of protein architecture.

Caetano-Anollés G, Caetano-Anollés D.

Genome Res. 2003 Jul;13(7):1563-71.

PMID:
12840035
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis.

Naganathan AN, Perez-Jimenez R, Muñoz V, Sanchez-Ruiz JM.

Phys Chem Chem Phys. 2011 Oct 14;13(38):17064-76. doi: 10.1039/c1cp20156e. Epub 2011 Jul 19.

PMID:
21769353
[PubMed - indexed for MEDLINE]
13.

A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation.

Wang M, Jiang YY, Kim KM, Qu G, Ji HF, Mittenthal JE, Zhang HY, Caetano-Anollés G.

Mol Biol Evol. 2011 Jan;28(1):567-82. doi: 10.1093/molbev/msq232. Epub 2010 Aug 30.

PMID:
20805191
[PubMed - indexed for MEDLINE]
Free Article
14.

How old is your fold?

Winstanley HF, Abeln S, Deane CM.

Bioinformatics. 2005 Jun;21 Suppl 1:i449-58.

PMID:
15961490
[PubMed - indexed for MEDLINE]
Free Article
15.

Finding evolutionary relations beyond superfamilies: fold-based superfamilies.

Matsuda K, Nishioka T, Kinoshita K, Kawabata T, Go N.

Protein Sci. 2003 Oct;12(10):2239-51.

PMID:
14500881
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Fold usage on genomes and protein fold evolution.

Abeln S, Deane CM.

Proteins. 2005 Sep 1;60(4):690-700.

PMID:
16001400
[PubMed - indexed for MEDLINE]
17.

Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution.

Abroi A, Gough J.

Bioessays. 2011 Aug;33(8):626-35. doi: 10.1002/bies.201000126. Epub 2011 Jun 1.

PMID:
21633962
[PubMed - indexed for MEDLINE]
18.

The largest protein observed to fold by two-state kinetic mechanism does not obey contact-order correlation.

Jones K, Wittung-Stafshede P.

J Am Chem Soc. 2003 Aug 13;125(32):9606-7.

PMID:
12904024
[PubMed - indexed for MEDLINE]
19.

Expanding the realm of ultrafast protein folding: gpW, a midsize natural single-domain with alpha+beta topology that folds downhill.

Fung A, Li P, Godoy-Ruiz R, Sanchez-Ruiz JM, Muñoz V.

J Am Chem Soc. 2008 Jun 11;130(23):7489-95. doi: 10.1021/ja801401a. Epub 2008 May 14.

PMID:
18479088
[PubMed - indexed for MEDLINE]
20.

Consequences of domain insertion on sequence-structure divergence in a superfold.

Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3381-7. doi: 10.1073/pnas.1305519110. Epub 2013 Aug 19.

PMID:
23959887
[PubMed - indexed for MEDLINE]
Free PMC Article

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