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Results: 1 to 20 of 53

1.

Protein domain hierarchy Gibbs sampling strategies.

Neuwald AF.

Stat Appl Genet Mol Biol. 2014 Jul 2. pii: /j/sagmb.ahead-of-print/sagmb-2014-0008/sagmb-2014-0008.xml. doi: 10.1515/sagmb-2014-0008. [Epub ahead of print]

PMID:
24988248
[PubMed - as supplied by publisher]
2.

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.

PMID:
24559108
[PubMed - in process]
3.

A Bayesian sampler for optimization of protein domain hierarchies.

Neuwald AF.

J Comput Biol. 2014 Mar;21(3):269-86. doi: 10.1089/cmb.2013.0099. Epub 2014 Feb 4.

PMID:
24494927
[PubMed - in process]
4.

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.

Neuwald AF, Lanczycki CJ, Marchler-Bauer A.

BMC Bioinformatics. 2012 Jun 22;13:144. doi: 10.1186/1471-2105-13-144.

PMID:
22726767
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms.

Neuwald AF.

Stat Appl Genet Mol Biol. 2011;10:Article 36. doi: 10.2202/1544-6115.1666. Epub 2011 Aug 4.

PMID:
22331370
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases.

Neuwald AF.

Biol Direct. 2010 Dec 3;5:66. doi: 10.1186/1745-6150-5-66.

PMID:
21129209
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Natural mutagenesis of human genomes by endogenous retrotransposons.

Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE.

Cell. 2010 Jun 25;141(7):1253-61. doi: 10.1016/j.cell.2010.05.020.

PMID:
20603005
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A typhus group-specific protease defies reductive evolution in rickettsiae.

Ammerman NC, Gillespie JJ, Neuwald AF, Sobral BW, Azad AF.

J Bacteriol. 2009 Dec;191(24):7609-13. doi: 10.1128/JB.01077-09. Epub 2009 Oct 9.

PMID:
19820087
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
19505947
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches.

Neuwald AF.

J Mol Biol. 2009 Jul 3;390(1):142-53. doi: 10.1016/j.jmb.2009.05.001. Epub 2009 May 7.

PMID:
19427324
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops.

Neuwald AF.

BMC Struct Biol. 2009 Mar 5;9:11. doi: 10.1186/1472-6807-9-11.

PMID:
19265520
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Evolution of allostery in the cyclic nucleotide binding module.

Kannan N, Wu J, Anand GS, Yooseph S, Neuwald AF, Venter JC, Taylor SS.

Genome Biol. 2007;8(12):R264.

PMID:
18076763
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Analogous regulatory sites within the alphaC-beta4 loop regions of ZAP-70 tyrosine kinase and AGC kinases.

Kannan N, Neuwald AF, Taylor SS.

Biochim Biophys Acta. 2008 Jan;1784(1):27-32. Epub 2007 Sep 29. Review.

PMID:
17977811
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module.

Kannan N, Haste N, Taylor SS, Neuwald AF.

Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1272-7. Epub 2007 Jan 16. Erratum in: Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):9130.

PMID:
17227859
[PubMed - indexed for MEDLINE]
Free PMC Article
17.
18.

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

Neuwald AF.

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

PMID:
16766187
[PubMed - indexed for MEDLINE]
19.
20.

Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component?

Kannan N, Neuwald AF.

J Mol Biol. 2005 Sep 2;351(5):956-72.

PMID:
16051269
[PubMed - indexed for MEDLINE]

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