Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins wit
- PDF / 1,564,984 Bytes
- 16 Pages / 595.276 x 793.701 pts Page_size
- 28 Downloads / 158 Views
SOFTWARE
Open Access
Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package Casey Cole , Caleb Parks, Julian Rachele and Homayoun Valafar* From The 20th International Conference on Bioinformatics & Computational Biology (BIOCOMP 2019) Las Vegas, NV, USA. 29 July-01 August 2019
* Correspondence: homayoun@cec. sc.edu Department of Computer Science and Engineering, University of South Carolina, M. Bert Storey Engineering and Innovation Center, 550 Assembly St, Columbia, SC 29201, USA
Abstract Background: Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR spectroscopy is time consuming and expensive. Residual Dipolar Couplings (RDCs) have become an alternate approach for structure calculation by NMR spectroscopy. In previous works, the software package REDCRAFT has been presented as a means of harnessing the information containing in RDCs for structure calculation of proteins. However, to meet its full potential, several improvements to REDCRAFT must be made. Results: In this work, we present improvements to REDCRAFT that include increased usability, better interoperability, and a more robust core algorithm. We have demonstrated the impact of the improved core algorithm in the successful folding of the protein 1A1Z with as high as ±4 Hz of added error. The REDCRAFT computed structure from the highly corrupted data exhibited less than 1.0 Å with respect to the X-ray structure. We have also demonstrated the interoperability of REDCRAFT in a few instances including with PDBMine to reduce the amount of required data in successful folding of proteins to unprecedented levels. Here we have demonstrated the successful folding of the protein 1D3Z (to within 2.4 Å of the X-ray structure) using only N-H RDCs from one alignment medium. Conclusions: The additional GUI features of REDCRAFT combined with the NEF compliance have significantly increased the flexibility and usability of this software package. The improvements of the core algorithm have substantially improved the robustness of REDCRAFT in utilizing less experimental data both in quality and quantity. Keywords: Protein folding, Residual dipolar coupling (RDC), Residual dipolar coupling based residue assembly and filter tool (REDCRAFT), Secondary structure, Data mining
© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated ot
Data Loading...
