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Software Developed by the Donald Lab

RDC-PANDA

Download | User Manual | License | Contact

Welcome to the website for the RDC-PANDA (RDC-based SSE PAcking with NOEs for Structure Determination and NOE Assignment) software. Here, you can download the newest version of the software, read the user manual and license agreement, or e-mail inquiries.

RDC-PANDA is a suite of programs for nuclear Overhauser effect (NOE) assignment and high-resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling (RDC) equations. RDC-PANDA is developed in the lab of Prof. Bruce Donald at Duke University. Citations to the primary papers for our work can be found here.

RDC-PANDA also comes with the RDC-ANALYTIC package built into it. RDC-ANALYTIC is a suite of programs for high-quality protein backbone fold determination from residual dipolar couplings (RDCs) (only two RDCs per residue are required) in one alignment medium, and a sparse set of nuclear Overhauser effect (NOE) data. Optionally, the latest version of RDC-ANALYTIC and its user manual can be downloaded from here.

RDC-PANDA is specifically designed for automated NMR NOE assignment and protein structure determination. It provides a novel approach for computing the initial structure template for NOE assignment by determining the protein backbone conformations from exact solutions to RDC equations, and systematically choosing rotamers based on NOE pattern matching. RDC-PANDA has been used to solve the new structures of the FF Domain 2 of human transcription elongation factor CA150 (RNA polymerase II C-terminal domain interacting protein) (FF2). The new NMR structures have been deposited into Protein Data Bank (PDB ID: 2KIQ). More details about RDC-PANDA can be found in the RDC-PANDA manual and our papers. A shorter list of the primary papers underlying our software can be found here.

RDC-ANALYTIC and RDC-PANDA are free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (optionally) any later version. RDC-ANALYTIC and RDC-PANDA are distributed in the hope that they will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Full licensing details, including citation requirements for the various different modules of the software, are found here.