We have developed a novel and robust approach for automatic and unsupervised simultaneous nuclear Overhauser effect (NOE) assignment and structure determination within the CS-Rosetta framework. Starting from unassigned peak lists and chemical shift assignments, autoNOE-Rosetta determines NOE cross-peak assignments and generates structural models. The approach tolerates incomplete and raw NOE peak lists as well as incomplete or partially incorrect chemical shift assignments, and its performance has been tested on 50 protein targets ranging from 50 to 200 residues in size. We find a significantly improved performance compared to established programs, particularly for larger proteins and for NOE data obtained on perdeuterated protein samples. X-ray crystallographic structures allowed comparison of Rosetta and conventional, PDB-deposited, NMR models in 20 of 50 test cases. The unsupervised autoNOE-Rosetta models were often of significantly higher accuracy than the corresponding expert-supervised NMR models deposited in the PDB. We also tested the method with unrefined peak lists and found that performance was nearly as good as for refined peak lists. Finally, demonstrating our methodâ??s remarkable robustness against problematic input data, we provided correct models for an incorrect PDB-deposited NMR solution structure.
[NMR paper] Automated robust and accurate assignment of protein resonances for solid state NMR.
Automated robust and accurate assignment of protein resonances for solid state NMR.
Automated robust and accurate assignment of protein resonances for solid state NMR.
J Biomol NMR. 2014 May 10;
Authors: Nielsen JT, Kulminskaya N, Bjerring M, Nielsen NC
Abstract
The process of resonance assignment represents a time-consuming and potentially error-prone bottleneck in structural studies of proteins by solid-state NMR (ssNMR). Software for the automation of this process is therefore of high interest. Procedures developed through...
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05-13-2014 03:11 PM
Alternative SAIL-Trp for robust aromatic signal assignment and determination of the Ï?2 conformation by intra-residue NOEs
Alternative SAIL-Trp for robust aromatic signal assignment and determination of the Ï?2 conformation by intra-residue NOEs
Abstract Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing -proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using...
Exclusively NOESY-based automated NMR assignment and structure determination of proteins
Exclusively NOESY-based automated NMR assignment and structure determination of proteins
Abstract A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information. Applied to two small proteins, the approach yielded structures that coincided closely with conventionally determined structures.
Content Type Journal Article
Pages 1-10
DOI 10.1007/s10858-011-9502-8
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04-01-2011 09:31 PM
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
J Biomol NMR. 2011 Mar 30;
Authors: Ikeya T, Jee JG, Shigemitsu Y, Hamatsu J, Mishima M, Ito Y, Kainosho M, Güntert P
A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information....
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03-31-2011 06:24 PM
[NMR paper] Rapid and accurate structure determination of coiled-coil domains using NMR dipolar couplings: application to cGMP-dependent protein kinase Ialpha.
Rapid and accurate structure determination of coiled-coil domains using NMR dipolar couplings: application to cGMP-dependent protein kinase Ialpha.
Related Articles Rapid and accurate structure determination of coiled-coil domains using NMR dipolar couplings: application to cGMP-dependent protein kinase Ialpha.
Protein Sci. 2005 Sep;14(9):2421-8
Authors: Schnell JR, Zhou GP, Zweckstetter M, Rigby AC, Chou JJ
Coiled-coil motifs play essential roles in protein assembly and molecular recognition, and are therefore the targets of many ongoing...
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12-01-2010 06:56 PM
[NMR paper] Protein NMR structure determination with automated NOE-identification in the NOESY sp
Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.
Related Articles Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.
J Biomol NMR. 2002 Nov;24(3):171-89
Authors: Herrmann T, Güntert P, Wüthrich K
Novel algorithms are presented for automated NOESY peak picking and NOE signal identification in homonuclear 2D and heteronuclear-resolved 3D -NOESY spectra during de novo protein structure determination by NMR,...
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11-24-2010 08:58 PM
Robust structure-based resonance assignment for functional protein studies by NMR
Abstract High-throughput functional protein NMR studies, like protein interactions or dynamics, require an automated approach for the assignment of the protein backbone. With the availability of a growing number of protein 3D structures, a new class of automated approaches, called structure-based assignment, has been developed quite recently. Structure-based approaches use primarily NMR input data that are not based on J-coupling and for which connections between residues are not limited by through bonds magnetization transfer efficiency. We present here a robust structure-based assignment...
Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta
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