ArticleJournal of biomolecular NMR2011
A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers.
Article in Journal of biomolecular NMR, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Defining essential charged residues in fibril formation of a lysosomal derived N-terminal α-synuclein truncation.Nature communications · 2025Article
- Manual and automatic assignment of two different Aβ40 amyloid fibril polymorphs using MAS solid-state NMR spectroscopy.Biomolecular NMR assignments · 2024Article
- POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data.Journal of structural biology: X · 2022Article
- Dynamic structural order of a low-complexity domain facilitates assembly of intermediate filaments.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Fused in Sarcoma: Properties, Self-Assembly and Correlation with Neurodegenerative Diseases.Molecules (Basel, Switzerland) · 2019Review
- Structural characterization of the D290V mutation site in hnRNPA2 low-complexity-domain polymers.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Backbone assignment of perdeuterated proteins by solid-state NMR using proton detection and ultrafast magic-angle spinning.Nature protocols · 2017Article
- INFOS: spectrum fitting software for NMR analysis.Journal of biomolecular NMR · 2017Article
- Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria.Journal of biomolecular NMR · 2016Article
- Aromatic spectral editing techniques for magic-angle-spinning solid-state NMR spectroscopy of uniformly (13)C-labeled proteins.Solid state nuclear magnetic resonance · 2015Article
- Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy.Protein science : a publication of the Protein Society · 2015Review
- MAS NMR of HIV-1 protein assemblies.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2015Article
- On the problem of resonance assignments in solid state NMR of uniformly ¹⁵N,¹³C-labeled proteins.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2015Article
- Magic angle spinning NMR of viruses.Progress in nuclear magnetic resonance spectroscopy · 2015Review
- Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data.Journal of biomolecular NMR · 2014Article
- Rapid proton-detected NMR assignment for proteins with fast magic angle spinning.Journal of the American Chemical Society · 2014Article
- VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra.Journal of biomolecular NMR · 2014Article
- Automated robust and accurate assignment of protein resonances for solid state NMR.Journal of biomolecular NMR · 2014Article
- Site-specific structural variations accompanying tubular assembly of the HIV-1 capsid protein.Journal of molecular biology · 2014Article
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3 authors.
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Abstract
We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes the connections that relate one signal list to another. As output, MCASSIGN2 produces a high-scoring sequential assignment of the multidimensional signals, using a score function that rewards good connections (i.e., agreement between relevant sets of chemical shifts in different signal lists) and penalizes bad connections, unassigned signals, and assignment gaps. Examination of a set of high-scoring assignments from a large number of independent runs allows one to determine whether a unique assignment exists for the entire sequence or parts thereof. We demonstrate the MCSA algorithm using two-dimensional (2D) and three-dimensional (3D) solid state NMR spectra of several model protein samples (α-spectrin SH3 domain and protein G/B1 microcrystals, HET-s(218-289) fibrils), obtained with magic-angle spinning and standard polarization transfer techniques. The MCSA algorithm and MCASSIGN2 program can accommodate arbitrary combinations of NMR spectra with arbitrary dimensionality, and can therefore be applied in many areas of solid state and solution NMR.
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