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BibTeX
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes
Journal of computational chemistry, 2011-02, Vol.32 (3), p.536-544
Latek, Dorota
Kolinski, Andrzej
2011
Details
Autor(en) / Beteiligte
Latek, Dorota
Kolinski, Andrzej
Titel
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes
Ist Teil von
Journal of computational chemistry, 2011-02, Vol.32 (3), p.536-544
Ort / Verlag
Hoboken: Wiley Subscription Services, Inc., A Wiley Company
Erscheinungsjahr
2011
Link zum Volltext
Quelle
MEDLINE
Beschreibungen/Notizen
Recent development of nuclear magnetic resonance (NMR) techniques provided new types of structural restraints that can be successfully used in fast and low‐cost global protein fold determination. Here, we present CABS‐NMR, an efficient protein modeling tool, which takes advantage of such structural restraints. The restraints are converted from original NMR data to fit the coarse grained protein representation of the C‐Alpha‐Beta‐Side‐group (CABS) algorithm. CABS is a Monte Carlo search algorithm that uses a knowledge‐based force field. Its versatile structure enables a variety of protein‐modeling protocols, including purely de novo folding, folding guided by restraints derived from template structures or, structure assembly based on experimental data. In particular, CABS‐NMR uses the distance and angular restraints set derived from various NMR experiments. This new modeling technique was successfully tested in structure determination of 10 globular proteins of size up to 216 residues, for which sparse NMR data were available. Additional detailed analysis was performed for a S100A1 protein. Namely, we successfully predicted Nuclear Overhauser Effect signals on the basis of low‐energy structures obtained from chemical shifts by CABS‐NMR. It has been observed that utility of chemical shifts and other types of experimental data (i.e. residual dipolar couplings and methyl‐methyl Nuclear Overhauser Effect signals) in the presented modeling pipeline depends mainly on size of a protein and complexity of its topology. In this work, we have provided tools for either post‐experiment processing of various kinds of NMR data or fast and low‐cost structural analysis in the still challenging field of new fold predictions. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Sprache
Englisch
Identifikatoren
ISSN: 0192-8651
eISSN: 1096-987X
DOI: 10.1002/jcc.21640
Titel-ID: cdi_proquest_miscellaneous_820789658
Format
–
Schlagworte
Algorithms
,
Animals
,
backbone reconstruction
,
Cattle
,
chemical shifts
,
de novo protein folding
,
Experiments
,
Magnetic Resonance Spectroscopy - methods
,
methyl-methyl NOEs
,
Models, Molecular
,
Molecular structure
,
Monte Carlo Method
,
Monte Carlo simulation
,
Monte Carlo simulations
,
NMR
,
Nuclear magnetic resonance
,
Protein Conformation
,
Protein Folding
,
protein structure prediction
,
Proteins - chemistry
,
reduced models
,
residual dipolar couplings
,
S100 Proteins - chemistry
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