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Items: 1 to 50 of 60

1.

Statistical investigations of protein residue direct couplings.

Neuwald AF, Altschul SF.

PLoS Comput Biol. 2018 Dec 31;14(12):e1006237. doi: 10.1371/journal.pcbi.1006237. eCollection 2018 Dec.

2.

Inferring joint sequence-structural determinants of protein functional specificity.

Neuwald AF, Aravind L, Altschul SF.

Elife. 2018 Jan 16;7. pii: e29880. doi: 10.7554/eLife.29880.

3.

Initial Cluster Analysis.

Altschul SF, Neuwald AF.

J Comput Biol. 2018 Feb;25(2):121-129. doi: 10.1089/cmb.2017.0050. Epub 2017 Aug 3.

4.

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

Neuwald AF, Altschul SF.

PLoS Comput Biol. 2016 Dec 21;12(12):e1005294. doi: 10.1371/journal.pcbi.1005294. eCollection 2016 Dec.

5.

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.

Neuwald AF, Altschul SF.

PLoS Comput Biol. 2016 May 18;12(5):e1004936. doi: 10.1371/journal.pcbi.1004936. eCollection 2016 May.

6.

Gleaning structural and functional information from correlations in protein multiple sequence alignments.

Neuwald AF.

Curr Opin Struct Biol. 2016 Jun;38:1-8. doi: 10.1016/j.sbi.2016.04.006. Epub 2016 May 12. Review.

PMID:
27179293
7.

Identification and classification of small molecule kinases: insights into substrate recognition and specificity.

Oruganty K, Talevich EE, Neuwald AF, Kannan N.

BMC Evol Biol. 2016 Jan 6;16:7. doi: 10.1186/s12862-015-0576-x.

8.

Protein domain hierarchy Gibbs sampling strategies.

Neuwald AF.

Stat Appl Genet Mol Biol. 2014 Aug;13(4):497-517. doi: 10.1515/sagmb-2014-0008.

PMID:
24988248
9.

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.

10.

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.

11.

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.

12.

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.

13.
14.

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.

15.

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.

16.

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.

17.

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.

18.
19.

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.

20.

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.

22.

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
23.

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.

25.

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

Neuwald AF.

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

PMID:
16766187
27.
28.

Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources.

Andersen JN, Del Vecchio RL, Kannan N, Gergel J, Neuwald AF, Tonks NK.

Methods. 2005 Jan;35(1):90-114. Review.

PMID:
15588990
29.
31.

Proteomic analysis of interchromatin granule clusters.

Saitoh N, Spahr CS, Patterson SD, Bubulya P, Neuwald AF, Spector DL.

Mol Biol Cell. 2004 Aug;15(8):3876-90. Epub 2004 May 28.

32.

Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells.

Ono T, Losada A, Hirano M, Myers MP, Neuwald AF, Hirano T.

Cell. 2003 Oct 3;115(1):109-21.

33.

Evolutionary clues to DNA polymerase III beta clamp structural mechanisms.

Neuwald AF.

Nucleic Acids Res. 2003 Aug 1;31(15):4503-16.

34.
35.
37.

A theory of information with special application to search problems.

Wilbur WJ, Neuwald AF.

Comput Chem. 2000 Jan;24(1):33-42.

PMID:
10642878
38.

Purification and biochemical characterization of interchromatin granule clusters.

Mintz PJ, Patterson SD, Neuwald AF, Spahr CS, Spector DL.

EMBO J. 1999 Aug 2;18(15):4308-20.

39.
40.

Sec14p-like domains in NF1 and Dbl-like proteins indicate lipid regulation of Ras and Rho signaling.

Aravind L, Neuwald AF, Ponting CP.

Curr Biol. 1999 Mar 25;9(6):R195-7. No abstract available.

41.
42.

A free energy analysis by unfolding applied to 125-mers on a cubic lattice.

Chung MS, Neuwald AF, Wilbur WJ.

Fold Des. 1998;3(1):51-65.

43.

Ataxin-2, global regulators of bacterial gene expression, and spliceosomal snRNP proteins share a conserved domain.

Neuwald AF, Koonin EV.

J Mol Med (Berl). 1998 Jan;76(1):3-5. No abstract available.

PMID:
9462862
45.

Barth syndrome may be due to an acyltransferase deficiency.

Neuwald AF.

Curr Biol. 1997 Aug 1;7(8):R465-6. No abstract available.

46.

A shared domain between a spindle assembly checkpoint protein and Ypt/Rab-specific GTPase-activators.

Neuwald AF.

Trends Biochem Sci. 1997 Jul;22(7):243-4. No abstract available.

PMID:
9255064
47.

GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein.

Neuwald AF, Landsman D.

Trends Biochem Sci. 1997 May;22(5):154-5. No abstract available.

PMID:
9175471
48.

Extracting protein alignment models from the sequence database.

Neuwald AF, Liu JS, Lipman DJ, Lawrence CE.

Nucleic Acids Res. 1997 May 1;25(9):1665-77.

49.

A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins.

Bork P, Hofmann K, Bucher P, Neuwald AF, Altschul SF, Koonin EV.

FASEB J. 1997 Jan;11(1):68-76.

PMID:
9034168
50.

Detection of likely transmembrane beta strand regions in sequences of mitochondrial pore proteins using the Gibbs sampler.

Mannella CA, Neuwald AF, Lawrence CE.

J Bioenerg Biomembr. 1996 Apr;28(2):163-9.

PMID:
9132415

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