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Items: 1 to 20 of 28

1.

Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings.

Simin M, Irausquin S, Cole CA, Valafar H.

J Biomol NMR. 2014 Dec;60(4):241-64. doi: 10.1007/s10858-014-9871-x. Epub 2014 Nov 18.

PMID:
25403759
2.

Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of Residual Dipolar Couplings.

Mukhopadhyay R, Irausquin S, Schmidt C, Valafar H.

J Bioinform Comput Biol. 2014 Feb;12(1):1450002. doi: 10.1142/S0219720014500024. Epub 2014 Jan 7.

3.

Advances in the REDCAT software package.

Schmidt C, Irausquin SJ, Valafar H.

BMC Bioinformatics. 2013 Oct 7;14:302. doi: 10.1186/1471-2105-14-302.

4.

Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.

Fahim A, Mukhopadhyay R, Yandle R, Prestegard JH, Valafar H.

Molecules. 2013 Aug 22;18(9):10162-88. doi: 10.3390/molecules180910162.

5.

An artificial neural network approach to improving the correlation between protein energetics and the backbone structure.

Fawcett TM, Irausquin SJ, Simin M, Valafar H.

Proteomics. 2013 Jan;13(2):230-8. doi: 10.1002/pmic.201200330. Epub 2012 Dec 23.

6.

Multiple structure alignment with msTALI.

Shealy P, Valafar H.

BMC Bioinformatics. 2012 May 20;13:105. doi: 10.1186/1471-2105-13-105.

7.

Backbone resonance assignment and order tensor estimation using residual dipolar couplings.

Shealy P, Liu Y, Simin M, Valafar H.

J Biomol NMR. 2011 Aug;50(4):357-69. doi: 10.1007/s10858-011-9521-5. Epub 2011 Jun 12.

8.

Simultaneous structure and dynamics of a membrane protein using REDCRAFT: membrane-bound form of Pf1 coat protein.

Shealy P, Simin M, Park SH, Opella SJ, Valafar H.

J Magn Reson. 2010 Nov;207(1):8-16. doi: 10.1016/j.jmr.2010.07.016. Epub 2010 Jul 30.

9.

Phage-induced alignment of membrane proteins enables the measurement and structural analysis of residual dipolar couplings with dipolar waves and lambda-maps.

Park SH, Son WS, Mukhopadhyay R, Valafar H, Opella SJ.

J Am Chem Soc. 2009 Oct 14;131(40):14140-1. doi: 10.1021/ja905640d.

10.

Efficient and accurate estimation of relative order tensors from lambda-maps.

Mukhopadhyay R, Miao X, Shealy P, Valafar H.

J Magn Reson. 2009 Jun;198(2):236-47. doi: 10.1016/j.jmr.2009.02.014. Epub 2009 Mar 5.

11.

Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application.

Miao X, Mukhopadhyay R, Valafar H.

J Magn Reson. 2008 Oct;194(2):202-11. doi: 10.1016/j.jmr.2008.07.005. Epub 2008 Jul 12.

12.

TALI: local alignment of protein structures using backbone torsion angles.

Miao X, Waddell PJ, Valafar H.

J Bioinform Comput Biol. 2008 Feb;6(1):163-81.

PMID:
18324751
13.

Rapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA).

Bansal S, Miao X, Adams MW, Prestegard JH, Valafar H.

J Magn Reson. 2008 May;192(1):60-8. doi: 10.1016/j.jmr.2008.01.014. Epub 2008 Feb 12.

14.

REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data.

Bryson M, Tian F, Prestegard JH, Valafar H.

J Magn Reson. 2008 Apr;191(2):322-34. doi: 10.1016/j.jmr.2008.01.007. Epub 2008 Jan 16.

15.

Determination of protein backbone structures from residual dipolar couplings.

Prestegard JH, Mayer KL, Valafar H, Benison GC.

Methods Enzymol. 2005;394:175-209.

16.

Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target.

Valafar H, Mayer KL, Bougault CM, LeBlond PD, Jenney FE Jr, Brereton PS, Adams MW, Prestegard JH.

J Struct Funct Genomics. 2004;5(4):241-54.

17.

Assessment of protein alignment using 1H-1H residual dipolar coupling measurements.

Wang J, Valafar H, Prestegard JH.

J Magn Reson. 2005 Jan;172(1):85-90.

PMID:
15589411
18.

NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system.

Di Lello P, Benison GC, Valafar H, Pitts KE, Summers AO, Legault P, Omichinski JG.

Biochemistry. 2004 Jul 6;43(26):8322-32.

PMID:
15222745
19.

REDCAT: a residual dipolar coupling analysis tool.

Valafar H, Prestegard JH.

J Magn Reson. 2004 Apr;167(2):228-41.

PMID:
15040978
20.

Assignment of protein backbone resonances using connectivity, torsion angles and 13Calpha chemical shifts.

Morris LC, Valafar H, Prestegard JH.

J Biomol NMR. 2004 May;29(1):1-9.

PMID:
15017135
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