ArticleJournal of magnetic resonance (San Diego, Calif. : 1997)2008
REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data.
Article in Journal of magnetic resonance (San Diego, Calif. : 1997), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Concurrent Identification and Characterization of Protein Structure and Continuous Internal Dynamics with REDCRAFT.Frontiers in molecular biosciences · 2022Article
- REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution.PLoS computational biology · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints.Structure (London, England : 1993) · 2019Article
- Validation of protein backbone structures calculated from NMR angular restraints using Rosetta.Journal of biomolecular NMR · 2019Article
- Integrating NOE and RDC using sum-of-squares relaxation for protein structure determination.Journal of biomolecular NMR · 2017Article
- FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data.Journal of biomolecular NMR · 2015Article
- Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings.Journal of biomolecular NMR · 2014Article
- Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of Residual Dipolar Couplings.Journal of bioinformatics and computational biology · 2014Article
- Advances in the REDCAT software package.BMC bioinformatics · 2013Article
- Quality assessment of protein NMR structures.Current opinion in structural biology · 2013Review
- Recommendations of the wwPDB NMR Validation Task Force.Structure (London, England : 1993) · 2013Article
- Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.Molecules (Basel, Switzerland) · 2013Article
- Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects.Progress in nuclear magnetic resonance spectroscopy · 2011Review
- RDC derived protein backbone resonance assignment using fragment assembly.Journal of biomolecular NMR · 2011Article
- Simultaneous structure and dynamics of a membrane protein using REDCRAFT: membrane-bound form of Pf1 coat protein.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2010Article
- Methods and estimations of uncertainties in single-molecule dynamic force spectroscopy.European biophysics journal : EBJ · 2009Article
- Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints.Progress in nuclear magnetic resonance spectroscopy · 2009Article
- Efficient and accurate estimation of relative order tensors from lambda-maps.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2009Article
- Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2008Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
REDCRAFT, a new open source software tool that accommodates the analysis of RDC data for simultaneous structure and dynamics characterization of proteins is presented in this article. Simultaneous consideration of structure and motion is believed to be necessary for accurate representation of the solution-state of a protein. REDCRAFT is designed to primarily utilize RDC data from multiple alignment media in two stages. During Stage-I, a list of possible torsion angles joining any two neighboring peptide planes is ranked based on their fitness to experimental constraints; in Stage-II, a dipeptide fragment is extended by addition of one peptide plane at a time. The algorithm adopted by REDCRAFT is very efficient and can produce a structure for an 80 residue protein within two hours on a typical desktop computer. REDCRAFT exhibits robustness with respect to noise and missing data. REDCRAFT describes the overall alignment of the molecule in the form of an order tensor matrix and is capable of identifying peptide fragments with internal dynamics. Identification of the location of internal motion will permit a more accurate structural representation. Experimental data from two proteins as well as simulated data are presented to illustrate the capabilities of REDCRAFT in both structure determination and identification of the dynamical regions.
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