PONDEROSA-C/S: client–server based software package for automated protein 3D structure determination

By Woonghee Lee, Jaime L. Stark, John L. Markley. 2014

58 citations recorded by the source corpus.

Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727–1728. doi:10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets (13C- and/or 15N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625–626. doi:10.1038/nmeth0909-625, 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1–2 days.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Predicting multiple conformations via sequence clustering and AlphaFold2 (2023, positive): “X-PLOR-NIH 75 -based calculations were used for all of the steps of structure calculations and refinement in the PONDEROSA C/S package 76 .”
POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data (2022, methodology): “To address this problem, we initially established a software platform, Integrative NMR (Lee et al., 2016a), whose key components, NMRFAM-SPARKY (Lee et al., 2015) and PONDEROSA-C/S (Lee et al., 2014), automate routine tasks in the workflow.”
The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data (2016, background): “C/S ) (Lee et al. 2014) automates the identiﬁcation of NOE cross peaks and the collection of torsion angle constraints.”
Integrative NMR for biomolecular research (2016, unknown): “Tasks are conducted by enhanced versions of two main software packages, NMRFAM-SPARKY (Lee et al. 2015) and PONDEROSA (Lee et al. 2011, 2014) in which old and new tools are integrated in efficient ways that emphasize visualization.”