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Items: 38

1.

Semantic Mediation to Improve Reproducibility for Biomolecular NMR Analysis.

Gryk MR, Ludäscher B.

Transform Digit Worlds (2018). 2018 Mar;10766:620-625. doi: 10.1007/978-3-319-78105-1_70. Epub 2018 Mar 15.

2.
3.

Curating Scientific Workflows for Biomolecular Nuclear Magnetic Resonance Spectroscopy.

Heintz D, Gryk MR.

Int J Digit Curation. 2018;13(1):286-293. doi: 10.2218/ijdc.v13i1.657. Epub 2019 Apr 19.

4.

NMRbox: A Resource for Biomolecular NMR Computation.

Maciejewski MW, Schuyler AD, Gryk MR, Moraru II, Romero PR, Ulrich EL, Eghbalnia HR, Livny M, Delaglio F, Hoch JC.

Biophys J. 2017 Apr 25;112(8):1529-1534. doi: 10.1016/j.bpj.2017.03.011.

5.

CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR-protein spectral assignment.

Fenwick M, Hoch JC, Ulrich E, Gryk MR.

J Biomol NMR. 2015 Oct;63(2):141-50. doi: 10.1007/s10858-015-9964-1. Epub 2015 Aug 8.

6.

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

Fenwick M, Weatherby G, Vyas J, Sesanker C, Martyn TO, Ellis HJ, Gryk MR.

J Biomol NMR. 2015 Jul;62(3):313-26. doi: 10.1007/s10858-015-9946-3. Epub 2015 Jun 12.

7.

Parser Combinators: a Practical Application for Generating Parsers for NMR Data.

Fenwick M, Weatherby G, Ellis HJ, Gryk MR.

Proc Int Conf Inf Technol New Gener. 2013. doi: 10.1109/ITNG.2013.39.

8.

Secondary structure, a missing component of sequence-based minimotif definitions.

Sargeant DP, Gryk MR, Maciejewski MW, Thapar V, Kundeti V, Rajasekaran S, Romero P, Dunker K, Li SC, Kaneko T, Schiller MR.

PLoS One. 2012;7(12):e49957. doi: 10.1371/journal.pone.0049957. Epub 2012 Dec 7.

9.

In support of the BMRB.

Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S.

Nat Struct Mol Biol. 2012 Sep;19(9):854-60. doi: 10.1038/nsmb.2371. No abstract available.

PMID:
22955930
10.

A Pipeline Software Architecture for NMR Spectrum Data Translation.

Ellis HJ, Weatherby G, Nowling RJ, Vyas J, Fenwick M, Gryk MR.

Comput Sci Eng. 2012 May 1;15(1):76-83.

11.

Iterative Development of an Application to Support Nuclear Magnetic Resonance Data Analysis of Proteins.

Ellis HJ, Nowling RJ, Vyas J, Martyn TO, Gryk MR.

Proc Int Conf Inf Technol New Gener. 2011 Apr 11:1014-1020.

12.

An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities.

Fenwick M, Sesanker C, Schiller MR, Ellis HJ, Hinman ML, Vyas J, Gryk MR.

Proc Int Conf Inf Technol New Gener. 2012;2012:89-94.

13.

Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences.

Mi T, Merlin JC, Deverasetty S, Gryk MR, Bill TJ, Brooks AW, Lee LY, Rathnayake V, Ross CA, Sargeant DP, Strong CL, Watts P, Rajasekaran S, Schiller MR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D252-60. doi: 10.1093/nar/gkr1189. Epub 2011 Dec 6.

14.

CONNJUR spectrum translator: an open source application for reformatting NMR spectral data.

Nowling RJ, Vyas J, Weatherby G, Fenwick MW, Ellis HJ, Gryk MR.

J Biomol NMR. 2011 May;50(1):83-9. doi: 10.1007/s10858-011-9497-1. Epub 2011 Mar 16.

15.

Biomolecular NMR data analysis.

Gryk MR, Vyas J, Maciejewski MW.

Prog Nucl Magn Reson Spectrosc. 2010 May;56(4):329-45. doi: 10.1016/j.pnmrs.2010.02.002. Review. No abstract available.

16.

MimoSA: a system for minimotif annotation.

Vyas J, Nowling RJ, Meusburger T, Sargeant D, Kadaveru K, Gryk MR, Kundeti V, Rajasekaran S, Schiller MR.

BMC Bioinformatics. 2010 Jun 16;11:328. doi: 10.1186/1471-2105-11-328.

17.

VENN, a tool for titrating sequence conservation onto protein structures.

Vyas J, Gryk MR, Schiller MR.

Nucleic Acids Res. 2009 Oct;37(18):e124. doi: 10.1093/nar/gkp616. Epub 2009 Aug 5.

18.

A proposed syntax for Minimotif Semantics, version 1.

Vyas J, Nowling RJ, Maciejewski MW, Rajasekaran S, Gryk MR, Schiller MR.

BMC Genomics. 2009 Aug 5;10:360. doi: 10.1186/1471-2164-10-360.

19.

Structural conservation of a short, functional, peptide-sequence motif.

Fox-Erlich S, Schiller MR, Gryk MR.

Front Biosci (Landmark Ed). 2009 Jan 1;14:1143-51. Review.

20.

Minimotif miner 2nd release: a database and web system for motif search.

Rajasekaran S, Balla S, Gradie P, Gryk MR, Kadaveru K, Kundeti V, Maciejewski MW, Mi T, Rubino N, Vyas J, Schiller MR.

Nucleic Acids Res. 2009 Jan;37(Database issue):D185-90. doi: 10.1093/nar/gkn865. Epub 2008 Oct 31.

21.

Comment on "magnetic resonance spectroscopy identifies neural progenitor cells in the live human brain".

Hoch JC, Maciejewski MW, Gryk MR.

Science. 2008 Aug 1;321(5889):640. doi: 10.1126/science.1153058.

22.

Local knowledge helps determine protein structures.

Gryk MR, Hoch JC.

Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4533-4. doi: 10.1073/pnas.0801069105. Epub 2008 Mar 19. No abstract available.

23.

Automatic maximum entropy spectral reconstruction in NMR.

Mobli M, Maciejewski MW, Gryk MR, Hoch JC.

J Biomol NMR. 2007 Oct;39(2):133-9. Epub 2007 Aug 15.

PMID:
17701276
24.

An automated tool for maximum entropy reconstruction of biomolecular NMR spectra.

Mobli M, Maciejewski MW, Gryk MR, Hoch JC.

Nat Methods. 2007 Jun;4(6):467-8. No abstract available.

PMID:
17538627
25.

Conceptual-level workflow modeling of scientific experiments using NMR as a case study.

Verdi KK, Ellis HJ, Gryk MR.

BMC Bioinformatics. 2007 Jan 30;8:31.

26.

Minimotif Miner: a tool for investigating protein function.

Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang CH, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, Schiller MR.

Nat Methods. 2006 Mar;3(3):175-7.

PMID:
16489333
27.

Delineation and analysis of the conceptual data model implied by the "IUPAC Recommendations for Biochemical Nomenclature".

Fox-Erlich S, Martyn TO, Ellis HJ, Gryk MR.

Protein Sci. 2004 Sep;13(9):2559-63. Epub 2004 Aug 4.

28.

Identification of small molecule synthetic inhibitors of DNA polymerase beta by NMR chemical shift mapping.

Hu HY, Horton JK, Gryk MR, Prasad R, Naron JM, Sun DA, Hecht SM, Wilson SH, Mullen GP.

J Biol Chem. 2004 Sep 17;279(38):39736-44. Epub 2004 Jul 15.

30.

Mapping of the interaction interface of DNA polymerase beta with XRCC1.

Gryk MR, Marintchev A, Maciejewski MW, Robertson A, Wilson SH, Mullen GP.

Structure. 2002 Dec;10(12):1709-20.

31.

1H, 13C and 15N resonance assignments for the perdeuterated 22 kD palm-thumb domain of DNA polymerase beta.

Gryk MR, Maciejewski MW, Robertson A, Mullen MA, Wilson SH, Mullen GP.

J Biomol NMR. 2002 Feb;22(2):197-8. No abstract available.

PMID:
11883786
32.

Solution structure of a viral DNA repair polymerase.

Maciejewski MW, Shin R, Pan B, Marintchev A, Denninger A, Mullen MA, Chen K, Gryk MR, Mullen GP.

Nat Struct Biol. 2001 Nov;8(11):936-41.

PMID:
11685238
33.

Solution structure of the single-strand break repair protein XRCC1 N-terminal domain.

Marintchev A, Mullen MA, Maciejewski MW, Pan B, Gryk MR, Mullen GP.

Nat Struct Biol. 1999 Sep;6(9):884-93.

PMID:
10467102
34.

Heteronuclear relaxation study of the PH domain of beta-spectrin: restriction of loop motions upon binding inositol trisphosphate.

Gryk MR, Abseher R, Simon B, Nilges M, Oschkinat H.

J Mol Biol. 1998 Jul 31;280(5):879-96.

PMID:
9671557
35.
36.

AV77 hinge mutation stabilizes the helix-turn-helix domain of trp repressor.

Gryk MR, Jardetzky O.

J Mol Biol. 1996 Jan 12;255(1):204-14.

PMID:
8568867
37.

Investigation of protein amide-proton exchange by 1H longitudinal spin relaxation.

Zheng Z, Gryk MR, Finucane MD, Jardetzky O.

J Magn Reson B. 1995 Sep;108(3):220-34.

PMID:
7670756
38.

Solution dynamics of the trp repressor: a study of amide proton exchange by T1 relaxation.

Gryk MR, Finucane MD, Zheng Z, Jardetzky O.

J Mol Biol. 1995 Mar 10;246(5):618-27.

PMID:
7877180

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