Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package

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...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 21; no. Suppl 9; pp. 204 - 16
Main Authors: Cole, Casey, Parks, Caleb, Rachele, Julian, Valafar, Homayoun
Format: Journal Article
Language:English
Published: London BioMed Central 03.12.2020
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
Algorithms
Analysis
Bioinformatics
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer programs
Couplings
Data Mining
Databases, Protein
Documentation
Folding
Graphical user interface
Interoperability
Life Sciences
Linux
Magnetic resonance spectroscopy
Magnetic Resonance Spectroscopy - methods
Mathematical analysis
Methods
Microarrays
Nef protein
NMR
NMR spectroscopy
Nuclear magnetic resonance
Nuclear Magnetic Resonance, Biomolecular
Peptides
Protein Conformation
Protein folding
Proteins
Proteins - chemistry
Residual dipolar coupling (RDC)
Residual dipolar coupling based residue assembly and filter tool (REDCRAFT)
Secondary structure
Software
Software packages
Software upgrading
Spectroscopy
Spectrum analysis
Structure
Usability
User interface
User-Computer Interface
United States
Residual dipolar coupling based residue assembly and filter tool (REDCRAFT)
Secondary structure
Data mining
Protein folding
Residual dipolar coupling (RDC)
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary: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.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-020-3522-x