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Items: 1 to 20 of 104

1.

Protein conformational diversity correlates with evolutionary rate.

Javier Zea D, Miguel Monzon A, Fornasari MS, Marino-Buslje C, Parisi G.

Mol Biol Evol. 2013 Jul;30(7):1500-3. doi: 10.1093/molbev/mst065. Epub 2013 Apr 5.

2.

Protein conformational diversity modulates sequence divergence.

Juritz E, Palopoli N, Fornasari MS, Fernandez-Alberti S, Parisi G.

Mol Biol Evol. 2013 Jan;30(1):79-87. doi: 10.1093/molbev/mss080. Epub 2012 Mar 6.

3.

On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions.

Juritz E, Fornasari MS, Martelli PL, Fariselli P, Casadio R, Parisi G.

BMC Genomics. 2012 Jun 18;13 Suppl 4:S5. doi: 10.1186/1471-2164-13-S4-S5.

4.

Conformational diversity and the emergence of sequence signatures during evolution.

Parisi G, Zea DJ, Monzon AM, Marino-Buslje C.

Curr Opin Struct Biol. 2015 Jun;32:58-65. doi: 10.1016/j.sbi.2015.02.005. Epub 2015 Mar 3. Review.

PMID:
25749052
5.

CoDNaS: a database of conformational diversity in the native state of proteins.

Monzon AM, Juritz E, Fornasari MS, Parisi G.

Bioinformatics. 2013 Oct 1;29(19):2512-4. doi: 10.1093/bioinformatics/btt405. Epub 2013 Jul 11.

6.

Protein evolution along phylogenetic histories under structurally constrained substitution models.

Arenas M, Dos Santos HG, Posada D, Bastolla U.

Bioinformatics. 2013 Dec 1;29(23):3020-8. doi: 10.1093/bioinformatics/btt530. Epub 2013 Sep 12.

7.
8.

Evolution of the correlation between expression divergence and protein divergence in mammals.

Warnefors M, Kaessmann H.

Genome Biol Evol. 2013;5(7):1324-35. doi: 10.1093/gbe/evt093.

9.

Heterotachy and functional shift in protein evolution.

Philippe H, Casane D, Gribaldo S, Lopez P, Meunier J.

IUBMB Life. 2003 Apr-May;55(4-5):257-65. Review.

10.

Three independent determinants of protein evolutionary rate.

Choi SS, Hannenhalli S.

J Mol Evol. 2013 Mar;76(3):98-111. doi: 10.1007/s00239-013-9543-6. Epub 2013 Feb 12. Review.

PMID:
23400388
11.
12.

Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers.

Barenboim M, Masso M, Vaisman II, Jamison DC.

Proteins. 2008 Jun;71(4):1930-9. doi: 10.1002/prot.21838.

PMID:
18186470
13.

Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.

Kuzmanic A, Zagrovic B.

Biophys J. 2010 Mar 3;98(5):861-71. doi: 10.1016/j.bpj.2009.11.011.

14.

Conformational strain in the hydrophobic core and its implications for protein folding and design.

Ventura S, Vega MC, Lacroix E, Angrand I, Spagnolo L, Serrano L.

Nat Struct Biol. 2002 Jun;9(6):485-93.

PMID:
12006985
15.

Constrained proper sampling of conformations of transition state ensemble of protein folding.

Lin M, Zhang J, Lu HM, Chen R, Liang J.

J Chem Phys. 2011 Feb 21;134(7):075103. doi: 10.1063/1.3519056.

16.

Simulating protein evolution in sequence and structure space.

Xia Y, Levitt M.

Curr Opin Struct Biol. 2004 Apr;14(2):202-7. Review.

PMID:
15093835
19.

Quantifying structural and functional restraints on amino acid substitutions in evolution of proteins.

Chelliah V, Blundell TL.

Biochemistry (Mosc). 2005 Aug;70(8):835-40.

PMID:
16212538
20.

Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account.

Mayrose I, Mitchell A, Pupko T.

J Mol Evol. 2005 Mar;60(3):345-53.

PMID:
15871045
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