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Items: 1 to 20 of 42

1.

More than meets the eye. Modern experimental techniques require increasingly sophisticated approaches to data visualization.

Rinaldi A.

EMBO Rep. 2012 Oct;13(10):895-9. doi: 10.1038/embor.2012.135. Epub 2012 Sep 18. No abstract available.

2.

Intuitive representation of surface properties of biomolecules using BioBlender.

Andrei RM, Callieri M, Zini MF, Loni T, Maraziti G, Pan MC, Zoppè M.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S16. doi: 10.1186/1471-2105-13-S4-S16.

3.

Phylo: a citizen science approach for improving multiple sequence alignment.

Kawrykow A, Roumanis G, Kam A, Kwak D, Leung C, Wu C, Zarour E; Phylo players, Sarmenta L, Blanchette M, Waldispühl J.

PLoS One. 2012;7(3):e31362. doi: 10.1371/journal.pone.0031362. Epub 2012 Mar 7.

4.

The case for open computer programs.

Ince DC, Hatton L, Graham-Cumming J.

Nature. 2012 Feb 22;482(7386):485-8. doi: 10.1038/nature10836.

PMID:
22358837
5.

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.

Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D.

Nat Biotechnol. 2012 Jan 22;30(2):190-2. doi: 10.1038/nbt.2109.

6.

Crystal structure of a monomeric retroviral protease solved by protein folding game players.

Khatib F, DiMaio F; Foldit Contenders Group; Foldit Void Crushers Group, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I, Thompson J, Popović Z, Jaskolski M, Baker D.

Nat Struct Mol Biol. 2011 Sep 18;18(10):1175-7. doi: 10.1038/nsmb.2119. Erratum in: Nat Struct Mol Biol. 2012 Mar;19(3):364.

7.

Acetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors.

Akdemir A, Rucktooa P, Jongejan A, Elk Rv, Bertrand S, Sixma TK, Bertrand D, Smit AB, Leurs R, de Graaf C, de Esch IJ.

Bioorg Med Chem. 2011 Oct 15;19(20):6107-19. doi: 10.1016/j.bmc.2011.08.028. Epub 2011 Aug 27.

PMID:
21920761
8.

Crystal structure of the Haemophilus influenzae Hap adhesin reveals an intercellular oligomerization mechanism for bacterial aggregation.

Meng G, Spahich N, Kenjale R, Waksman G, St Geme JW 3rd.

EMBO J. 2011 Aug 12;30(18):3864-74. doi: 10.1038/emboj.2011.279.

9.

Crystal structure of α-galactosidase from Lactobacillus acidophilus NCFM: insight into tetramer formation and substrate binding.

Fredslund F, Hachem MA, Larsen RJ, Sørensen PG, Coutinho PM, Lo Leggio L, Svensson B.

J Mol Biol. 2011 Sep 23;412(3):466-80. doi: 10.1016/j.jmb.2011.07.057. Epub 2011 Jul 30.

PMID:
21827767
10.

GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.

Chavent M, Vanel A, Tek A, Levy B, Robert S, Raffin B, Baaden M.

J Comput Chem. 2011 Oct;32(13):2924-35. doi: 10.1002/jcc.21861. Epub 2011 Jul 7.

PMID:
21735559
11.

Structure of the ATP synthase catalytic complex (F(1)) from Escherichia coli in an autoinhibited conformation.

Cingolani G, Duncan TM.

Nat Struct Mol Biol. 2011 Jun;18(6):701-7. doi: 10.1038/nsmb.2058. Epub 2011 May 22.

12.

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O.

J Comput Chem. 2011 Jul 30;32(10):2319-27. doi: 10.1002/jcc.21787. Epub 2011 Apr 15.

13.

ePMV embeds molecular modeling into professional animation software environments.

Johnson GT, Autin L, Goodsell DS, Sanner MF, Olson AJ.

Structure. 2011 Mar 9;19(3):293-303. doi: 10.1016/j.str.2010.12.023.

14.

The power of many.

Sansom C.

Nat Biotechnol. 2011 Mar;29(3):201-3. doi: 10.1038/nbt.1792. No abstract available.

PMID:
21390017
15.

GPU-powered tools boost molecular visualization.

Chavent M, Lévy B, Krone M, Bidmon K, Nominé JP, Ertl T, Baaden M.

Brief Bioinform. 2011 Nov;12(6):689-701. doi: 10.1093/bib/bbq089. Epub 2011 Feb 9.

PMID:
21310717
16.

Designed ankyrin repeat protein binders for the crystallization of AcrB: plasticity of the dominant interface.

Monroe N, Sennhauser G, Seeger MA, Briand C, Grütter MG.

J Struct Biol. 2011 May;174(2):269-81. doi: 10.1016/j.jsb.2011.01.014. Epub 2011 Feb 4.

PMID:
21296164
17.

Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.

Wojtas M, Peralta B, Ondiviela M, Mogni M, Bell SD, Abrescia NG.

Biochem Soc Trans. 2011 Jan;39(1):25-30. doi: 10.1042/BST0390025. Review.

PMID:
21265742
18.

Cytoscape 2.8: new features for data integration and network visualization.

Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T.

Bioinformatics. 2011 Feb 1;27(3):431-2. doi: 10.1093/bioinformatics/btq675. Epub 2010 Dec 12.

19.

Importance of Arg-599 of β-galactosidase (Escherichia coli) as an anchor for the open conformations of Phe-601 and the active-site loop.

Dugdale ML, Vance ML, Wheatley RW, Driedger MR, Nibber A, Tran A, Huber RE.

Biochem Cell Biol. 2010 Dec;88(6):969-79. doi: 10.1139/O10-144.

PMID:
21102659
20.

Animating the model figure.

Iwasa JH.

Trends Cell Biol. 2010 Dec;20(12):699-704. doi: 10.1016/j.tcb.2010.08.005. Epub 2010 Sep 9.

PMID:
20832316

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