PARNMR: A GenApp-Generated Science Gateway for Comprehensive Analysis of
Paramagnetic Effects in Biomolecular NMR Data
Andy Guan1, Matthew Casertano1,2, Cheol Jeong3, Emre H Brookes3, David
Fushman1
1. Department of Chemistry and Biochemistry, University of Maryland,
College Park, Maryland
2. Montgomery Blair High School, Silver Spring, Maryland
3. Department of Chemistry & Biochemistry, University of Montana, Missoula,
Montana
Attachment of paramagnetic labels to biological macromolecules has become a
powerful tool for obtaining information on their structure, dynamics, and
function. PARNMR is a versatile software package that enables researchers
to perform accurate and comprehensive analysis of NMR data acquired in the
presence of paramagnetic labels in order to determine three-dimensional
structure of biological macromolecules (proteins and nucleic acids). The
package allows analysis of pseudo-contact shifts (PCS), residual dipolar
couplings (RDC), and paramagnetic relaxation enhancements (PRE). PARNMR
also includes tools for prediction of RDCs and PCSs and for deriving
structural constraints for structure determination and refinement of
macromolecular complexes and for analysis of conformational ensembles.
However, until recently, these programs existed as separate modules written
in Matlab, which inevitably limited their accessibility to and use by the
broad scientific community. Using the GenApp framework for scientific
gateways (https://genapp.rocks), we are developing a science gateway for
PARNMR that provides advanced computational functionalities, streamlines
data input, storage, and output, and enables interactive 2D and 3D plotting
and visualization. These features will improve the user experience and
broaden the number of potential users of this gateway. This work involved
translation of the existing Matlab code into Python code and development of
new tools that improved data analysis and visualization. We will present
specific examples illustrating data input, functionality, and output
visualization. The software generated in this project will be available to
all applications developed using the GenApp framework and will also be made
publicly available as a stand-alone component. We believe that others in
science gateways related to biological structural community will be able to
use these new tools to advance their research capabilities and to enhance
their research experience. As next steps, we intend to integrate this
package with other GenApp applications and modules for small-angle
scattering and NMR data analysis. We also believe that our GenApp-based
PARNMR gateway will set an example that will stimulate other research
groups to share their scientific computer programs in a similar way.
This work was supported by an NSF grant and SGCI internship award.
