Literature DB >> 28445744

NMRbox: A Resource for Biomolecular NMR Computation.

Mark W Maciejewski1, Adam D Schuyler1, Michael R Gryk1, Ion I Moraru2, Pedro R Romero3, Eldon L Ulrich3, Hamid R Eghbalnia3, Miron Livny4, Frank Delaglio5, Jeffrey C Hoch6.   

Abstract

Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users.
Copyright © 2017 Biophysical Society. All rights reserved.

Mesh:

Year:  2017        PMID: 28445744      PMCID: PMC5406371          DOI: 10.1016/j.bpj.2017.03.011

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  22 in total

1.  Consistent blind protein structure generation from NMR chemical shift data.

Authors:  Yang Shen; Oliver Lange; Frank Delaglio; Paolo Rossi; James M Aramini; Gaohua Liu; Alexander Eletsky; Yibing Wu; Kiran K Singarapu; Alexander Lemak; Alexandr Ignatchenko; Cheryl H Arrowsmith; Thomas Szyperski; Gaetano T Montelione; David Baker; Ad Bax
Journal:  Proc Natl Acad Sci U S A       Date:  2008-03-07       Impact factor: 11.205

2.  SHIFTX2: significantly improved protein chemical shift prediction.

Authors:  Beomsoo Han; Yifeng Liu; Simon W Ginzinger; David S Wishart
Journal:  J Biomol NMR       Date:  2011-03-30       Impact factor: 2.835

3.  Enhancing reproducibility for computational methods.

Authors:  Victoria Stodden; Marcia McNutt; David H Bailey; Ewa Deelman; Yolanda Gil; Brooks Hanson; Michael A Heroux; John P A Ioannidis; Michela Taufer
Journal:  Science       Date:  2016-12-09       Impact factor: 47.728

4.  Modern spectrum analysis in nuclear magnetic resonance: alternatives to the Fourier transform.

Authors:  J C Hoch
Journal:  Methods Enzymol       Date:  1989       Impact factor: 1.600

5.  Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

Authors:  Enis Afgan; Brad Chapman; Margita Jadan; Vedran Franke; James Taylor
Journal:  Curr Protoc Bioinformatics       Date:  2012-06

6.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

7.  Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

Authors:  Joseph M Courtney; Qing Ye; Anna E Nesbitt; Ming Tang; Marcus D Tuttle; Eric D Watt; Kristin M Nuzzio; Lindsay J Sperling; Gemma Comellas; Joseph R Peterson; James H Morrissey; Chad M Rienstra
Journal:  Structure       Date:  2015-09-10       Impact factor: 5.006

8.  NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.

Authors:  Woonghee Lee; Marco Tonelli; John L Markley
Journal:  Bioinformatics       Date:  2014-12-12       Impact factor: 6.937

9.  Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.

Authors:  Gijs van der Schot; Alexandre M J J Bonvin
Journal:  J Biomol NMR       Date:  2015-05-17       Impact factor: 2.835

10.  Integrative NMR for biomolecular research.

Authors:  Woonghee Lee; Gabriel Cornilescu; Hesam Dashti; Hamid R Eghbalnia; Marco Tonelli; William M Westler; Samuel E Butcher; Katherine A Henzler-Wildman; John L Markley
Journal:  J Biomol NMR       Date:  2016-03-29       Impact factor: 2.835

View more
  99 in total

1.  Structural Basis for Graded Inhibition of CREB:DNA Interactions by Multisite Phosphorylation.

Authors:  Sergey Shnitkind; Maria A Martinez-Yamout; H Jane Dyson; Peter E Wright
Journal:  Biochemistry       Date:  2018-12-13       Impact factor: 3.162

2.  Replacement of the Distal Histidine Reveals a Noncanonical Heme Binding Site in a 2-on-2 Hemoglobin.

Authors:  Dillon B Nye; Juliette T J Lecomte
Journal:  Biochemistry       Date:  2018-09-28       Impact factor: 3.162

3.  Importance of time-ordered non-uniform sampling of multi-dimensional NMR spectra of Aβ1-42 peptide under aggregating conditions.

Authors:  Jinfa Ying; C Ashley Barnes; John M Louis; Ad Bax
Journal:  J Biomol NMR       Date:  2019-08-12       Impact factor: 2.835

4.  Concomitant disorder and high-affinity zinc binding in the human zinc- and iron-regulated transport protein 4 intracellular loop.

Authors:  Elizabeth M Bafaro; Mark W Maciejewski; Jeffrey C Hoch; Robert E Dempski
Journal:  Protein Sci       Date:  2019-03-12       Impact factor: 6.725

5.  Conservation and Divergence of the I-Domain Inserted into the Ubiquitous HK97 Coat Protein Fold in P22-Like Bacteriophages.

Authors:  Therese N Tripler; Anne R Kaplan; Andrei T Alexandrescu; Carolyn M Teschke
Journal:  J Virol       Date:  2019-04-17       Impact factor: 5.103

6.  Semantic Mediation to Improve Reproducibility for Biomolecular NMR Analysis.

Authors:  Michael R Gryk; Bertram Ludäscher
Journal:  Transform Digit Worlds (2018)       Date:  2018-03-15

7.  1H, 13C, 15N backbone resonance assignments of the apo and holo forms of the ABC transporter solute binding protein PiuA from Streptococcus pneumoniae.

Authors:  Katherine A Edmonds; Yifan Zhang; Daniel J Raines; Anne-K Duhme-Klair; David P Giedroc
Journal:  Biomol NMR Assign       Date:  2020-06-03       Impact factor: 0.746

8.  Rational design of cell-permeable cyclic peptides containing a d-Pro-l-Pro motif.

Authors:  Jin Wen; Hui Liao; Kye Stachowski; Jordan P Hempfling; Ziqing Qian; Chunhua Yuan; Mark P Foster; Dehua Pei
Journal:  Bioorg Med Chem       Date:  2020-08-18       Impact factor: 3.641

9.  Structural and functional analyses of the N-terminal domain of the A subunit of a Bacillus megaterium spore germinant receptor.

Authors:  Yunfeng Li; Kai Jin; Abigail Perez-Valdespino; Kyle Federkiewicz; Andrew Davis; Mark W Maciejewski; Peter Setlow; Bing Hao
Journal:  Proc Natl Acad Sci U S A       Date:  2019-05-21       Impact factor: 11.205

10.  Reaching the sparse-sampling limit for reconstructing a single peak in a 2D NMR spectrum using iterated maps.

Authors:  Robert L Blum; Jared Rovny; J Patrick Loria; Sean E Barrett
Journal:  J Biomol NMR       Date:  2019-07-10       Impact factor: 2.835

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.