Related ArticlesNMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.
Bioinformatics. 2015 Oct 26;
Authors: Ryu H, Lim G, Sung BH, Lee J
Abstract
Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores.
AVAILABILITY: NMRe is available at http://psb.kobic.re.kr/nmre/ CONTACT: jinhyuk@kribb.re.krSupplementary Information.
PMID: 26504145 [PubMed - as supplied by publisher]
[NMR paper] NMR structure validation in relation to dynamics and structure determination.
NMR structure validation in relation to dynamics and structure determination.
NMR structure validation in relation to dynamics and structure determination.
Prog Nucl Magn Reson Spectrosc. 2014 Oct;82C:27-38
Authors: Vranken WF
Abstract
NMR spectroscopy is a key technique for understanding the behaviour of proteins, especially highly dynamic proteins that adopt multiple conformations in solution. Overall, protein structures determined from NMR spectroscopy data constitute just over 10% of the Protein Data Bank archive. This...
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12-03-2014 04:05 PM
NMR structure validation in relation to dynamics and structure determination
NMR structure validation in relation to dynamics and structure determination
Publication date: Available online 26 August 2014
Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br>
Author(s): Wim F. Vranken</br>
NMR spectroscopy is a key technique for understanding the behaviour of proteins, especially highly dynamic proteins that adopt multiple conformations in solution. Overall, protein structures determined from NMR spectroscopy data constitute just over 10% of the Protein Data Bank archive. This review covers the validation of these NMR protein...
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08-28-2014 10:09 AM
[NMR paper] High-Quality NMR Structure of Human Anti-Apoptotic Protein Domain Mcl-1(171-327) for Cancer Drug Design.
High-Quality NMR Structure of Human Anti-Apoptotic Protein Domain Mcl-1(171-327) for Cancer Drug Design.
Related Articles High-Quality NMR Structure of Human Anti-Apoptotic Protein Domain Mcl-1(171-327) for Cancer Drug Design.
PLoS One. 2014;9(5):e96521
Authors: Liu G, Poppe L, Aoki K, Yamane H, Lewis J, Szyperski T
Abstract
A high-quality NMR solution structure is presented for protein hMcl-1(171-327) which comprises residues 171-327 of the human anti-apoptotic protein Mcl-1 (hMcl-1). Since this construct contains the three...
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05-03-2014 10:42 PM
[NMR paper] Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality a
Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.
Related Articles Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.
J Am Chem Soc. 2005 Feb 16;127(6):1665-74
Authors: Huang YJ, Powers R, Montelione GT
One of the most important challenges in modern protein NMR is the development of fast and sensitive structure quality assessment measures that can be...
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11-24-2010 11:14 PM
[BMNRC community] The PSIPRED Protein Structure Prediction Server
The PSIPRED Protein Structure Prediction Server
http://bioinf.cs.ucl.ac.uk/psipred/
Go to BMNRC community to find more info about this topic.
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09-04-2010 06:53 AM
Fully automated high-quality NMR structure determination of small (2)H-enriched prote
Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.
Related Articles Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.
J Struct Funct Genomics. 2010 Aug 24;
Authors: Tang Y, Schneider WM, Shen Y, Raman S, Inouye M, Baker D, Roth MJ, Montelione GT
Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands...
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08-25-2010 02:04 PM
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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NMR software
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07-20-2005 05:44 PM
NMR RPF: new NMR quality assessment scores
Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.
Huang YJ, Powers R, Montelione GT.
Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers University, Northeast Structural Genomics Consortium, and Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5368, USA.
J Am Chem Soc. 2005 Feb 16;127(6):1665-74.
Abstract:
NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.
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