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Items: 1 to 20 of 81

1.

The CHAIN program: forging evolutionary links to underlying mechanisms.

Neuwald AF.

Trends Biochem Sci. 2007 Nov;32(11):487-93. Epub 2007 Oct 24.

PMID:
17962021
2.

Bayesian shadows of molecular mechanisms cast in the light of evolution.

Neuwald AF.

Trends Biochem Sci. 2006 Jul;31(7):374-82.

PMID:
16766187
3.

Molecular evolution before the origin of species.

Davis BK.

Prog Biophys Mol Biol. 2002 May-Jul;79(1-3):77-133. Review.

PMID:
12225777
6.

Structural and functional restraints in the evolution of protein families and superfamilies.

Gong S, Worth CL, Bickerton GR, Lee S, Tanramluk D, Blundell TL.

Biochem Soc Trans. 2009 Aug;37(Pt 4):727-33. doi: 10.1042/BST0370727. Review.

PMID:
19614584
7.

Empirical and structural models for insertions and deletions in the divergent evolution of proteins.

Benner SA, Cohen MA, Gonnet GH.

J Mol Biol. 1993 Feb 20;229(4):1065-82.

PMID:
8445636
8.
9.
10.

A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motif.

Koonin EV.

J Mol Biol. 1993 Feb 20;229(4):1165-74. Erratum in: J Mol Biol 1993 Aug 5;232(3):1013.

PMID:
8445645
11.

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

Neuwald AF.

Bioinformatics. 2009 Aug 1;25(15):1869-75. doi: 10.1093/bioinformatics/btp342. Epub 2009 Jun 8. Erratum in: Bioinformatics. 2009 Nov 15;25(22):3047.

13.

Evolutionary bases of carbohydrate recognition and substrate discrimination in the ROK protein family.

Conejo MS, Thompson SM, Miller BG.

J Mol Evol. 2010 Jun;70(6):545-56. doi: 10.1007/s00239-010-9351-1. Epub 2010 May 30.

PMID:
20512568
14.

Inferring property selection pressure from positional residue conservation.

Hoberman R, Klein-Seetharaman J, Rosenfeld R.

Appl Bioinformatics. 2004;3(2-3):167-79.

PMID:
15693742
15.

Evaluating, comparing, and interpreting protein domain hierarchies.

Neuwald AF.

J Comput Biol. 2014 Apr;21(4):287-302. doi: 10.1089/cmb.2013.0098. Epub 2014 Feb 21.

16.

Identification of functionally conserved residues with the use of entropy-variability plots.

Oliveira L, Paiva PB, Paiva AC, Vriend G.

Proteins. 2003 Sep 1;52(4):544-52.

PMID:
12910454
17.

Extracting hydrogen-bond signature patterns from protein structure data.

Prasad T, Subramanian T, Hariharaputran S, Chaitra HS, Chandra N.

Appl Bioinformatics. 2004;3(2-3):125-35.

PMID:
15693738
18.

Amino acid substitution during functionally constrained divergent evolution of protein sequences.

Benner SA, Cohen MA, Gonnet GH.

Protein Eng. 1994 Nov;7(11):1323-32.

PMID:
7700864
20.

Evolutionary divergence plots of homologous proteins.

Brouillet S, Risler JL, Hénaut A, Slonimski PP.

Biochimie. 1992 Jun;74(6):571-80.

PMID:
1520737

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