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Items: 1 to 20 of 92

1.

Evolution: a guide to perturb protein function and networks.

Lichtarge O, Wilkins A.

Curr Opin Struct Biol. 2010 Jun;20(3):351-9. doi: 10.1016/j.sbi.2010.04.002. Epub 2010 May 3. Review.

2.

Evolutionary trace for prediction and redesign of protein functional sites.

Wilkins A, Erdin S, Lua R, Lichtarge O.

Methods Mol Biol. 2012;819:29-42. doi: 10.1007/978-1-61779-465-0_3.

3.

Accurate and scalable identification of functional sites by evolutionary tracing.

Lichtarge O, Yao H, Kristensen DM, Madabushi S, Mihalek I.

J Struct Funct Genomics. 2003;4(2-3):159-66. Review.

PMID:
14649300
4.

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.

Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A.

PLoS Comput Biol. 2009 Jan;5(1):e1000267. doi: 10.1371/journal.pcbi.1000267. Epub 2009 Jan 23.

5.

An accurate, sensitive, and scalable method to identify functional sites in protein structures.

Yao H, Kristensen DM, Mihalek I, Sowa ME, Shaw C, Kimmel M, Kavraki L, Lichtarge O.

J Mol Biol. 2003 Feb 7;326(1):255-61.

PMID:
12547207
6.

Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

Bershtein S, Serohijos AW, Shakhnovich EI.

Curr Opin Struct Biol. 2017 Feb;42:31-40. doi: 10.1016/j.sbi.2016.10.013. Epub 2016 Oct 31. Review.

7.

Detecting protein function and protein-protein interactions from genome sequences.

Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D.

Science. 1999 Jul 30;285(5428):751-3.

8.
9.

Predicting functional divergence in protein evolution by site-specific rate shifts.

Gaucher EA, Gu X, Miyamoto MM, Benner SA.

Trends Biochem Sci. 2002 Jun;27(6):315-21. Review.

PMID:
12069792
10.
11.

An integrated view of molecular coevolution in protein-protein interactions.

Lovell SC, Robertson DL.

Mol Biol Evol. 2010 Nov;27(11):2567-75. doi: 10.1093/molbev/msq144. Epub 2010 Jun 14. Review.

PMID:
20551042
12.

A structural perspective of compensatory evolution.

Ivankov DN, Finkelstein AV, Kondrashov FA.

Curr Opin Struct Biol. 2014 Jun;26:104-12. doi: 10.1016/j.sbi.2014.05.004. Epub 2014 Jun 28. Review.

13.

Evolution of protein interactions: from interactomes to interfaces.

Andreani J, Guerois R.

Arch Biochem Biophys. 2014 Jul 15;554:65-75. doi: 10.1016/j.abb.2014.05.010. Epub 2014 May 20. Review.

PMID:
24853495
14.

Multispecific recognition: mechanism, evolution, and design.

Erijman A, Aizner Y, Shifman JM.

Biochemistry. 2011 Feb 8;50(5):602-11. doi: 10.1021/bi101563v. Epub 2011 Jan 13. Review.

PMID:
21229991
15.

Using Evolution to Guide Protein Engineering: The Devil IS in the Details.

Swint-Kruse L.

Biophys J. 2016 Jul 12;111(1):10-8. doi: 10.1016/j.bpj.2016.05.030. Review.

16.

Sequences and topology: evolution of proteins and evolution of computational approaches.

Teichmann SA, Grishin N.

Curr Opin Struct Biol. 2010 Jun;20(3):333-4. doi: 10.1016/j.sbi.2010.04.004. Epub 2010 May 17. No abstract available.

17.

Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information.

Wang K, Horst JA, Cheng G, Nickle DC, Samudrala R.

PLoS Comput Biol. 2008 Sep 26;4(9):e1000181. doi: 10.1371/journal.pcbi.1000181.

18.

Evolution of the protein repertoire.

Chothia C, Gough J, Vogel C, Teichmann SA.

Science. 2003 Jun 13;300(5626):1701-3.

PMID:
12805536
19.

Computational prediction of protein-protein interactions.

Obenauer JC, Yaffe MB.

Methods Mol Biol. 2004;261:445-68. Review.

PMID:
15064475
20.

Using evolutionary information to find specificity-determining and co-evolving residues.

Kolesov G, Mirny LA.

Methods Mol Biol. 2009;541:421-48. doi: 10.1007/978-1-59745-243-4_18. Review.

PMID:
19381538

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