ArticleJournal of biomolecular NMR2015
MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data.
Article in Journal of biomolecular NMR, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 48 citations in OpenAlex.
- Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.Nature communications · 2026Article
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- Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs.RSC advances · 2023Review
- Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment.Chemical science · 2021Article
- Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins.Molecules (Basel, Switzerland) · 2021Review
- Using Cross-Correlated Spin Relaxation to Characterize Backbone Dihedral Angle Distributions of Flexible Protein Segments.Chemphyschem : a European journal of chemical physics and physical chemistry · 2021Article
- Detecting anisotropic segmental dynamics in disordered proteins by cross-correlated spin relaxation.Magnetic resonance (Gottingen, Germany) · 2021Article
- A novel high-dimensional NMR experiment for resolving protein backbone dihedral angle ambiguities.Journal of biomolecular NMR · 2020Article
- Salient Features of Monomeric Alpha-Synuclein Revealed by NMR Spectroscopy.Biomolecules · 2020Review
- Unravelling the effect ofChemical science · 2020Article
- Molecular Interactions of the Polysialytransferase Domain (PSTD) in ST8Sia IV with CMP-Sialic Acid and Polysialic Acid Required for Polysialylation of the Neural Cell Adhesion Molecule Proteins: An NMR Study.International journal of molecular sciences · 2020Article
- Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias.The journal of physical chemistry. B · 2019Article
- Entropy and Information within Intrinsically Disordered Protein Regions.Entropy (Basel, Switzerland) · 2019Article
- Efficient Ensemble Refinement by Reweighting.Journal of chemical theory and computation · 2019Article
- Applications of In-Cell NMR in Structural Biology and Drug Discovery.International journal of molecular sciences · 2019Review
- Modeling the Early Stages of Phase Separation in Disordered Elastin-like Proteins.Biophysical journal · 2018Article
- Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins.Protein science : a publication of the Protein Society · 2018Article
- A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP.Journal of biomolecular NMR · 2016Article
- Quantitative evaluation of positive ϕ angle propensity in flexible regions of proteins from three-bond J couplings.Physical chemistry chemical physics : PCCP · 2016Article
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Authors and funding
5 authors at 3 institutions in 3 countries.
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Abstract
MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts ((15)N, (13)C(α), and (13)C'), six types of J couplings ((3)JHNHα, (3)JC'C', (3)JC'Hα, (1)JHαCα, (2)JCαN and (1)JCαN), as well as the (15)N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3.
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