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Items: 1 to 20 of 94

1.

Semiautomated model building for RNA crystallography using a directed rotameric approach.

Keating KS, Pyle AM.

Proc Natl Acad Sci U S A. 2010 May 4;107(18):8177-82. doi: 10.1073/pnas.0911888107. Epub 2010 Apr 19.

2.

RCrane: semi-automated RNA model building.

Keating KS, Pyle AM.

Acta Crystallogr D Biol Crystallogr. 2012 Aug;68(Pt 8):985-95. doi: 10.1107/S0907444912018549. Epub 2012 Jul 17.

3.

Geometric properties of nucleic acids with potential for autobuilding.

Gruene T, Sheldrick GM.

Acta Crystallogr A. 2011 Jan;67(Pt 1):1-8. doi: 10.1107/S0108767310039140. Epub 2010 Nov 11.

4.

RNA backbone is rotameric.

Murray LJ, Arendall WB 3rd, Richardson DC, Richardson JS.

Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):13904-9. Epub 2003 Nov 11.

5.

Computational Methods for RNA Structure Validation and Improvement.

Jain S, Richardson DC, Richardson JS.

Methods Enzymol. 2015;558:181-212. doi: 10.1016/bs.mie.2015.01.007. Epub 2015 Apr 2.

PMID:
26068742
6.

Automatic modeling of protein backbones in electron-density maps via prediction of Calpha coordinates.

Ioerger TR, Sacchettini JC.

Acta Crystallogr D Biol Crystallogr. 2002 Dec;58(Pt 12):2043-54. Epub 2002 Nov 23.

PMID:
12454463
7.

Features and development of Coot.

Emsley P, Lohkamp B, Scott WG, Cowtan K.

Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501. doi: 10.1107/S0907444910007493. Epub 2010 Mar 24.

8.

RNA Structure Refinement Using the ERRASER-Phenix Pipeline.

Chou FC, Echols N, Terwilliger TC, Das R.

Methods Mol Biol. 2016;1320:269-82. doi: 10.1007/978-1-4939-2763-0_17.

9.

A probabilistic approach to protein backbone tracing in electron density maps.

DiMaio F, Shavlik J, Phillips GN.

Bioinformatics. 2006 Jul 15;22(14):e81-9.

PMID:
16873525
10.

Sequence-dependent DNA structure: the role of the sugar-phosphate backbone.

Packer MJ, Hunter CA.

J Mol Biol. 1998 Jul 17;280(3):407-20.

PMID:
9665845
11.

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

Brunger AT, Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams PD, Levitt M, Schröder GF.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):391-403. doi: 10.1107/S090744491104978X. Epub 2012 Mar 16.

12.

RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.

Wang X, Kapral G, Murray L, Richardson D, Richardson J, Snoeyink J.

J Math Biol. 2008 Jan;56(1-2):253-78. Epub 2007 Mar 31.

13.

RNA backbone rotamers--finding your way in seven dimensions.

Murray LJ, Richardson JS, Arendall WB, Richardson DC.

Biochem Soc Trans. 2005 Jun;33(Pt 3):485-7.

PMID:
15916548
14.

Model-building strategies for low-resolution X-ray crystallographic data.

Karmali AM, Blundell TL, Furnham N.

Acta Crystallogr D Biol Crystallogr. 2009 Feb;65(Pt 2):121-7. doi: 10.1107/S0907444908040006. Epub 2009 Jan 20.

15.

Building of RNA and DNA double helices into electron density.

Pavelcik F, Schneider B.

Acta Crystallogr D Biol Crystallogr. 2008 Jun;64(Pt 6):620-6. doi: 10.1107/S0907444908007075. Epub 2008 May 14.

PMID:
18560149
16.

Crystallographic protein model-building on the web.

Gopal K, McKee E, Romo T, Pai R, Smith J, Sacchettini J, Ioerger T.

Bioinformatics. 2007 Feb 1;23(3):375-7. Epub 2006 Nov 30.

PMID:
17138588
17.

Real-space protein-model completion: an inverse-kinematics approach.

van den Bedem H, Lotan I, Latombe JC, Deacon AM.

Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):2-13. Epub 2004 Dec 17.

PMID:
15608370
18.
19.

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).

Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM; RNA Ontology Consortium..

RNA. 2008 Mar;14(3):465-81. doi: 10.1261/rna.657708. Epub 2008 Jan 11.

20.

Matching the crystallographic structure of ribosomal protein S7 to a three-dimensional model of the 16S ribosomal RNA.

Tanaka I, Nakagawa A, Hosaka H, Wakatsuki S, Mueller F, Brimacombe R.

RNA. 1998 May;4(5):542-50.

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