Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 103

1.

Conformation dependence of backbone geometry in proteins.

Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA.

Structure. 2009 Oct 14;17(10):1316-25. doi: 10.1016/j.str.2009.08.012.

PMID:
19836332
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
20606264
[PubMed - indexed for MEDLINE]
Free PMC Article
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 May 31. doi: 10.1111/febs.12860. [Epub ahead of print]

PMID:
24890778
[PubMed - as supplied by publisher]
4.

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites.

Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL Jr, Karplus PA.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):449-53. doi: 10.1073/pnas.1107115108. Epub 2011 Dec 23.

PMID:
22198840
[PubMed - indexed for MEDLINE]
Free PMC Article
5.
6.

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC.

J Mol Biol. 1999 Jan 29;285(4):1711-33.

PMID:
9917407
[PubMed - indexed for MEDLINE]
7.

A new force field (ECEPP-05) for peptides, proteins, and organic molecules.

Arnautova YA, Jagielska A, Scheraga HA.

J Phys Chem B. 2006 Mar 16;110(10):5025-44.

PMID:
16526746
[PubMed - indexed for MEDLINE]
8.

Peptide bond distortions from planarity: new insights from quantum mechanical calculations and peptide/protein crystal structures.

Improta R, Vitagliano L, Esposito L.

PLoS One. 2011;6(9):e24533. doi: 10.1371/journal.pone.0024533. Epub 2011 Sep 16.

PMID:
21949726
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Chaintweak: sampling from the neighbourhood of a protein conformation.

Singh R, Bergert B.

Pac Symp Biocomput. 2005:52-63.

PMID:
15759613
[PubMed - indexed for MEDLINE]
10.

Relaxation of backbone bond geometry improves protein energy landscape modeling.

Conway P, Tyka MD, DiMaio F, Konerding DE, Baker D.

Protein Sci. 2014 Jan;23(1):47-55.

PMID:
24265211
[PubMed - indexed for MEDLINE]
11.

Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry.

Lipsitz RS, Sharma Y, Brooks BR, Tjandra N.

J Am Chem Soc. 2002 Sep 4;124(35):10621-6.

PMID:
12197765
[PubMed - indexed for MEDLINE]
12.

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.

PMID:
21795811
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC.

Proteins. 2003 Feb 15;50(3):437-50.

PMID:
12557186
[PubMed - indexed for MEDLINE]
14.

A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions.

Shapovalov MV, Dunbrack RL Jr.

Structure. 2011 Jun 8;19(6):844-58. doi: 10.1016/j.str.2011.03.019.

PMID:
21645855
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Modeling protein loops using a phi i + 1, psi i dimer database.

Sudarsanam S, DuBose RF, March CJ, Srinivasan S.

Protein Sci. 1995 Jul;4(7):1412-20.

PMID:
7670382
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

Bell JA, Ho KL, Farid R.

Acta Crystallogr D Biol Crystallogr. 2012 Aug;68(Pt 8):935-52. doi: 10.1107/S0907444912017453. Epub 2012 Jul 17.

PMID:
22868759
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.

Vila JA, Scheraga HA.

Acc Chem Res. 2009 Oct 20;42(10):1545-53. doi: 10.1021/ar900068s.

PMID:
19572703
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Experimentally observed conformation-dependent geometry and hidden strain in proteins.

Karplus PA.

Protein Sci. 1996 Jul;5(7):1406-20.

PMID:
8819173
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Protein imperfections: separating intrinsic from extrinsic variation of torsion angles.

Butterfoss GL, Richardson JS, Hermans J.

Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):88-98. Epub 2004 Dec 17.

PMID:
15608380
[PubMed - indexed for MEDLINE]
20.

Strategy for supplementing structure calculations using limited data with hydrophobic distance restraints.

Alexandrescu AT.

Proteins. 2004 Jul 1;56(1):117-29.

PMID:
15162492
[PubMed - indexed for MEDLINE]

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk