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Items: 27

1.

A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream.

Moriarty NW, Tronrud DE, Adams PD, Karplus PA.

Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):176-9. doi: 10.1107/S2059798315022408. Epub 2016 Jan 1.

2.

Residue-level global and local ensemble-ensemble comparisons of protein domains.

Clark SA, Tronrud DE, Karplus PA.

Protein Sci. 2015 Sep;24(9):1528-42. doi: 10.1002/pro.2714. Epub 2015 Jun 22.

3.

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement.

Moriarty NW, Tronrud DE, Adams PD, Karplus PA.

FEBS J. 2014 Sep;281(18):4061-71. doi: 10.1111/febs.12860. Epub 2014 Jun 17.

4.

Reinterpretation of the electron density at the site of the eighth bacteriochlorophyll in the FMO protein from Pelodictyon phaeum.

Tronrud DE, Allen JP.

Photosynth Res. 2012 Apr;112(1):71-4. doi: 10.1007/s11120-012-9735-8. Epub 2012 Mar 29.

5.

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution.

Tronrud DE, Karplus PA.

Acta Crystallogr D Biol Crystallogr. 2011 Aug;67(Pt 8):699-706. doi: 10.1107/S090744491102292X. Epub 2011 Jul 12.

6.

Iron-containing urease in a pathogenic bacterium.

Carter EL, Tronrud DE, Taber SR, Karplus PA, Hausinger RP.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13095-9. doi: 10.1073/pnas.1106915108. Epub 2011 Jul 25.

7.

Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.

Tronrud DE, Berkholz DS, Karplus PA.

Acta Crystallogr D Biol Crystallogr. 2010 Jul;66(Pt 7):834-42. doi: 10.1107/S0907444910019207. Epub 2010 Jun 19.

8.

Lessons from the lysozyme of phage T4.

Baase WA, Liu L, Tronrud DE, Matthews BW.

Protein Sci. 2010 Apr;19(4):631-41. doi: 10.1002/pro.344. Review.

9.

The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria.

Tronrud DE, Wen J, Gay L, Blankenship RE.

Photosynth Res. 2009 May;100(2):79-87. doi: 10.1007/s11120-009-9430-6. Epub 2009 May 13.

PMID:
19437128
10.
11.

Sorting the chaff from the wheat at the PDB.

Tronrud DE, Matthews BW.

Protein Sci. 2009 Jan;18(1):2-5. doi: 10.1002/pro.13. No abstract available.

12.

Introduction to macromolecular refinement.

Tronrud DE.

Methods Mol Biol. 2007;364:231-54.

PMID:
17172769
13.

Introduction to macromolecular refinement.

Tronrud DE.

Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2156-68. Epub 2004 Nov 26.

PMID:
15572769
14.
15.
16.

Refined structure of Cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity.

Ohlendorf DH, Tronrud DE, Matthews BW.

J Mol Biol. 1998 Jul 3;280(1):129-36.

PMID:
9653036
17.

TNT refinement package.

Tronrud DE.

Methods Enzymol. 1997;277:306-19. No abstract available.

PMID:
9379924
18.

Structural comparison suggests that thermolysin and related neutral proteases undergo hinge-bending motion during catalysis.

Holland DR, Tronrud DE, Pley HW, Flaherty KM, Stark W, Jansonius JN, McKay DB, Matthews BW.

Biochemistry. 1992 Nov 24;31(46):11310-6.

PMID:
1445869
19.

Analysis of the effectiveness of proline substitutions and glycine replacements in increasing the stability of phage T4 lysozyme.

Nicholson H, Tronrud DE, Becktel WJ, Matthews BW.

Biopolymers. 1992 Nov;32(11):1431-41.

PMID:
1457724
20.

Conjugate-direction minimization: an improved method for the refinement of macromolecules.

Tronrud DE.

Acta Crystallogr A. 1992 Nov 1;48 ( Pt 6):912-6.

PMID:
1418827
21.

Structural basis for the action of thermolysin.

Tronrud DE, Roderick SL, Matthews BW.

Matrix Suppl. 1992;1:107-11.

PMID:
1480010
22.

Contributions of left-handed helical residues to the structure and stability of bacteriophage T4 lysozyme.

Nicholson H, Söderlind E, Tronrud DE, Matthews BW.

J Mol Biol. 1989 Nov 5;210(1):181-93.

PMID:
2511328
23.
24.

Structures of two thermolysin-inhibitor complexes that differ by a single hydrogen bond.

Tronrud DE, Holden HM, Matthews BW.

Science. 1987 Jan 30;235(4788):571-4.

PMID:
3810156
25.
26.
27.

Structural analysis of the inhibition of thermolysin by an active-site-directed irreversible inhibitor.

Holmes MA, Tronrud DE, Matthews BW.

Biochemistry. 1983 Jan 4;22(1):236-40.

PMID:
6830761

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