Related ArticlesCSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.
Nucleic Acids Res. 2015 May 15;
Authors: Hafsa NE, Arndt D, Wishart DS
Abstract
The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, ?-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, ?-strands, coil regions, five common ?-turns (type I, II, I', II' and VIII), ? hairpins as well as interior and edge ?-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.
PMID: 25979265 [PubMed - as supplied by publisher]
[NMR paper] Modeling Proteins Using a Super-Secondary Structure Library and NMR Chemical Shift Information.
Modeling Proteins Using a Super-Secondary Structure Library and NMR Chemical Shift Information.
Related Articles Modeling Proteins Using a Super-Secondary Structure Library and NMR Chemical Shift Information.
Structure. 2013 May 14;
Authors: Menon V, Vallat BK, Dybas JM, Fiser A
Abstract
A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs)...
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05-21-2013 02:34 PM
Modeling Proteins Using a Super-Secondary Structure Library and NMR Chemical Shift Information
Modeling Proteins Using a Super-Secondary Structure Library and NMR Chemical Shift Information
Publication date: Available online 16 May 2013
Source:Structure</br>
Author(s): Vilas Menon , Brinda*K. Vallat , Joseph*M. Dybas , Andras Fiser</br>
A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build...
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05-16-2013 06:05 PM
Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps
Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps
Available online 18 March 2013
Publication year: 2013
Source:Journal of Molecular Structure</br>
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NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from...
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03-19-2013 12:58 AM
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Abstract Unravelling the complex correlation between chemical shifts of 13 C α, 13 C β, 13 C�, 1 H α, 15 N, 1 H N atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous...
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11-14-2011 08:45 AM
[NMR paper] Secondary structural effects on protein NMR chemical shifts.
Secondary structural effects on protein NMR chemical shifts.
Related Articles Secondary structural effects on protein NMR chemical shifts.
J Biomol NMR. 2004 Nov;30(3):233-44
Authors: Wang Y
For an amino acid in protein, its chemical shift, delta(phi, psi)(s), is expressed as a function of its backbone torsion angles (phi and psi) and secondary state (s): delta(phi, psi)(s=deltaphi, psi)_coil+Deltadelta(phi, psi)_s), where delta(phi, psi)(coil) represents its chemical shift at coil state (s=coil); Delta delta(phi, psi)(s) (s=sheet or helix) is...
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11-24-2010 10:03 PM
The predictive accuracy of secondary chemical shifts is more affected by protein seco
Abstract Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Î?δ) values, measured as the difference between experimental and random coil chemical shifts (RCCS). Most published random coil data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane proteins. Two new RCCS sets are presented here, determined in dimethyl sulfoxide (DMSO) and chloroform:methanol:water (4:4:1 by volume) at 298 K. A web-based program, CS-CHEMeleon, has been implemented to...
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08-14-2010 04:19 AM
PECAN server - protein secondary structure via NMR
http://bija.nmrfam.wisc.edu/PECAN/Pecan.jpg
Link to the PECAN server
Instructions about PECAN input files
Info from the PECAN website:PECAN offers a new approach to secondary structure identification that achieves excellent results.
PECAN is a component in a suite of tools for high-throughput structure determination using NMR.
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07-20-2005 05:44 PM
PSSI: secondary structure from chemical shifts
Link to PSSI program
Reference and abstract:
Probability-based protein secondary structure identification using combined NMR chemical-shift data.
Wang Y, Jardetzky O.
Division of Chemical Biology, Department of Molecular Pharmacology, Stanford University, Stanford, California 94305, USA.
CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.
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