The ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically selects consistent restraints. Hamiltonian replica exchange...
[NMR paper] An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling
An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling
Paramagnetic nuclear magnetic resonance (NMR) methods have emerged as powerful tools for structure determination of large, sparsely protonated proteins. However traditional applications face several challenges, including a need for large datasets to offset the sparsity of restraints, the difficulty in accounting for the conformational heterogeneity of the spin-label, and noisy experimental data. Here we propose an integrative approach to structure determination combining...
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[NMR paper] PRE-driven Protein NMR Structures: an Alternative Approach in Highly Paramagnetic Systems.
PRE-driven Protein NMR Structures: an Alternative Approach in Highly Paramagnetic Systems.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7388-69-wiley-full-text.png Related Articles PRE-driven Protein NMR Structures: an Alternative Approach in Highly Paramagnetic Systems.
FEBS J. 2020 Oct 30;:
Authors: Trindade IB, Invernici M, Cantini F, Louro RO, Piccioli M
Abstract
Metalloproteins play key roles across biology, and knowledge of their structure is essential to understand their...
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[NMR paper] NMR-Based Modeling and Refinement of Protein 3D Structures.
NMR-Based Modeling and Refinement of Protein 3D Structures.
Related Articles NMR-Based Modeling and Refinement of Protein 3D Structures.
Methods Mol Biol. 2015;1215:351-80
Authors: Vranken WF, Vuister GW, Bonvin AM
Abstract
NMR is a well-established method to characterize the structure and dynamics of biomolecules in solution. High-quality structures can now be produced thanks to both experimental advances and computational developments that incorporate new NMR parameters and improved protocols and force fields in the structure...
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Protein structure modeling using sparse NMR data [Biophysics and Computational Biology]
Protein structure modeling using sparse NMR data
Thompson, J. M., Sgourakis, N. G., Liu, G., Rossi, P., Tang, Y., Mills, J. L., Szyperski, T., Montelione, G. T., Baker, D....
Date: 2012-06-19
While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that...
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06-20-2012 02:28 AM
[NMR paper] Folding Trp-cage to NMR resolution native structure using a coarse-grained protein mo
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model.
Related Articles Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model.
Biophys J. 2005 Jan;88(1):147-55
Authors: Ding F, Buldyrev SV, Dokholyan NV
We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20-residue protein--Trp-cage--from a fully extended conformation. We demonstrate the ability...
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11-24-2010 10:03 PM
[NMR paper] An automated approach for clustering an ensemble of NMR-derived protein structures in
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Related Articles An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Protein Eng. 1996 Nov;9(11):1063-5
Authors: Kelley LA, Gardner SP, Sutcliffe MJ
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[NMR paper] An approach to protein homology modelling based on an ensemble of NMR structures: app
An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.
Related Articles An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.
Protein Eng. 1995 Jul;8(7):615-25
Authors: Adzhubei AA, Laughton CA, Neidle S
A new approach has been developed to reduce multiple protein structures obtained from NMR structure analysis to a smaller number of representative structures which still reflect the structural diversity of...
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08-22-2010 03:41 AM
[NMR paper] SESAME: a least-squares approach to the evaluation of protein structures computed fro
SESAME: a least-squares approach to the evaluation of protein structures computed from NMR data.
Related Articles SESAME: a least-squares approach to the evaluation of protein structures computed from NMR data.
J Biomol NMR. 1993 May;3(3):355-60
Authors: Yang JX, Havel TF
A method is proposed for defining a probability distribution on an ensemble of protein conformations from a 2D NOE spectrum, while at the same time back-calculating the experimental spectrum from the ensemble. This enables one to assess the relative quality and significance...
A coarse-grained approach to NMR-data-assisted modeling of protein structures
Linear Mode
