areca.nmrfam.wisc.edu

ARECA@NMRFAM

NOESY contacts analyses ▼. Assessment of the REliability of Chemical shift Assignments) as a part of NMRFAM software packages. Uses information from the through-space internuclear proximities contained in NOE spectra of the protein. ARECA uses a truth model that indicates expectation probabilities of NOESY contacts between intra and inter-resdiue protons. These probabilities are available through our NOESY Contact Probabilities ( NCP. Chemical Shift Assignments [ instruction. 1 Select a file. The ARECA p...

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ARECA@NMRFAM | areca.nmrfam.wisc.edu Reviews

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NOESY contacts analyses ▼. Assessment of the REliability of Chemical shift Assignments) as a part of NMRFAM software packages. Uses information from the through-space internuclear proximities contained in NOE spectra of the protein. ARECA uses a truth model that indicates expectation probabilities of NOESY contacts between intra and inter-resdiue protons. These probabilities are available through our NOESY Contact Probabilities ( NCP. Chemical Shift Assignments [ instruction. 1 Select a file. The ARECA p...

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1 noesy contacts probabilities

2 short range contacts analyses

3 noesy restraints analyses

4 examples

5 nmrfam servers

6 nmrfam

7 the areca

8 webserver

9 n noesy peak list

10 c noesy d

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ARECA@NMRFAM | areca.nmrfam.wisc.edu Reviews

https://areca.nmrfam.wisc.edu

NOESY contacts analyses ▼. Assessment of the REliability of Chemical shift Assignments) as a part of NMRFAM software packages. Uses information from the through-space internuclear proximities contained in NOE spectra of the protein. ARECA uses a truth model that indicates expectation probabilities of NOESY contacts between intra and inter-resdiue protons. These probabilities are available through our NOESY Contact Probabilities ( NCP. Chemical Shift Assignments [ instruction. 1 Select a file. The ARECA p...

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areca.nmrfam.wisc.edu

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ARECA-NOESY Contacts Probabilities@NMRFAM

http://areca.nmrfam.wisc.edu/ncp

NOESY contacts analyses ▼. NMRFAM Servers ▼. In NMR studies of proteins it is useful to have the probability of NOESY contacts between two protons. We have developed a module for validating chemical shifts assignments against NOESY data ( ARECA. And as a part of this module we calculated the probabilities of short-range NOESY contacts in two ways:. We used structures deposited at the PACSY. Database and filter them by the use of the MolProbility. In addition we used the TINKER molecular modeling. A stati...

2

ARECA@NMRFAM

http://areca.nmrfam.wisc.edu/example.html

NOESY contacts analyses ▼. NMRFAM Servers ▼. Examples from the second round of CASD-NMR. HR2876B with refined peak lists. BMRB NMRSTAR v3.1. Backbone and ali/arom side chain. Opens in a new tab). 2D scatter plot of probabilities vs. confidences:. Opens in a new tab). Opens in a new tab). Opens in a new tab). HR2876B with raw peak lists. BMRB NMRSTAR v3.1. Backbone and ali/arom side chain. Opens in a new tab). 2D scatter plot of probabilities vs. confidences:. Opens in a new tab). Opens in a new tab).

3

ARECA@NMRFAM

http://areca.nmrfam.wisc.edu/ncp/ncp_analysis

NOESY contacts analyses ▼. NMRFAM Servers ▼. Statistics on the expected number of short-range NOESY contacts. Provides probabilities of NOESY contacts. In ARECA. ALA (Avg. 13.277). CYS (Avg. 13.492). ASP (Avg. 13.522). GLU (Avg. 13.869). PHE (Avg. 14.506). GLY (Avg. 11.805). HIS (Avg. 14.347). ILE (Avg. 14.460). LYS (Avg. 14.702). LEU (Avg. 14.676). MET (Avg. 14.304). ASN (Avg. 13.902). PRO (Avg. 13.745). GLN (Avg. 14.155). ARG (Avg. 14.783). SER (Avg. 13.357). THR (Avg. 13.902). VAL (Avg. 14.268).

4

ARECA@NMRFAM

http://areca.nmrfam.wisc.edu/help.html

NOESY contacts analyses ▼. NMRFAM Servers ▼. For any question or concern please contact Hesam Dashti (dashti@nmrfam.wisc.edu). Chemical Shift Assignments options. BMRB NMRSTAR v2.1:. In the NMRSTAR v2.1 files the chemical shift assignments should start with a header that explains the data contents. In the following example the necessary tags that ARECA looks for are tagged in an example of NMRSAR v2.1 file:. Atom shift assign ID. Residue author seq code. Chem shift value error. Chem shift ambiguity code.

5

ARECA-NOESY Contacts Probabilities@NMRFAM

http://areca.nmrfam.wisc.edu/ncp/nrg_analysis

NOESY contacts analyses ▼. NMRFAM Servers ▼. Statistical Analysis on Protein NOESY Distance Restraints. Caluclating statistics on the number of reported NOESY distance restraints per residue for proteins. We downloaded the parsed simple NOESY distance database from the NRG ( http:/ restraintsgrid.bmrb.wisc.edu/. The entries containing nucleic acids were removed. 5836 entries (proteins) were used for our statistical analysis. The histogram of the ratio is shown in Fig. 1.

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zavot.nmrfam.wisc.edu

Mani Tools - PINE Server

http://zavot.nmrfam.wisc.edu//RNA

RNA Probabilistic Assignment of Imino Resonance Shifts. RNA-PAIRS is part of a multi-step collaborative project aimed at automating RNA chemical shift assignments and structure determination. The first step here is an automated tool for the probabilistic assignment of RNA imino proton resonances. And validation of secondary structure. The beta version provided here accepts as input the user's initial guess of the RNA secondary structure, as well as peak lists from. For input data are:. N HSQC and 2D.

zavot.nmrfam.wisc.edu

ADAPT-NMR

http://zavot.nmrfam.wisc.edu//ADAPT-NMR

Bahrami A, Tonelli M, Sahu SC, Singarapu KK, Eghbalnia HR, et al. (2012) Robust, Integrated Computational Control of NMR Experiments to Achieve Optimal Assignment by ADAPT-NMR. PLoS ONE 7(3): e33173. doi:10.1371/journal.pone.0033173 (PLOS One link). ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) is a fully automated method for integration of protein NMR data collection, chemical shift assignment, and secondary structure determination. Lee W, Bahrami A, ...

zavot.nmrfam.wisc.edu

Mani Tools - PINE Server

http://zavot.nmrfam.wisc.edu//LACS

Assignment outlier detection and correction of errors in referencing. Liya Wang, Hamid R. Eghbal. Nia, Arash Bahrami, John L. Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications" , Journal of Biomolecular NMR. Description of LACS input and output files can be found here. A service offered by the National Magnetic Resonance Facility at Madison. Updated OCTOBER 2010. Upload files to LACS Server.

zavot.nmrfam.wisc.edu

Mani Tools - PINE Server

http://zavot.nmrfam.wisc.edu//PECAN

Probabilistic secondary structure determination of protein. Hamid R. Eghbalnia, Liya Wang, Arash Bahrami, Amir Assadi, John L. Markley,. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements , Journal of Biomolecular NMR. Description of PECAN input and output files can be found below. Input file (NMRFAM-Sparky two-letter-code: n6). Output file (NDPPlot input included). Upload files to PECAN Server. Upload files to PECAN Server.

pacsy.nmrfam.wisc.edu

PACSY main page

http://pacsy.nmrfam.wisc.edu/index.html

Example of Pacsy Maker. Example of Pacsy Analyzer. CSV-formatted version of PACSY is now downloadable from here (Monthly Updated). MolProbity Analysis is now added as MOLPROB DB table! PACSY reference correction and statistics from Dr. Keith Fritzsching. PACSY RAMA is downloadable. Check our download page. Try PACSY web service below:. Tip Use PACSY Analyzer program to create SQL query easy. J Biomol NMR. 2012 Oct;54(2):169-79. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL. Last Updated: July 16, 2015.

pine.nmrfam.wisc.edu

Mani Tools - PINE Server

http://pine.nmrfam.wisc.edu//LACS

Assignment outlier detection and correction of errors in referencing. Liya Wang, Hamid R. Eghbal. Nia, Arash Bahrami, John L. Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications" , Journal of Biomolecular NMR. Description of LACS input and output files can be found here. A service offered by the National Magnetic Resonance Facility at Madison. Updated OCTOBER 2010. Upload files to LACS Server.

pine.nmrfam.wisc.edu

ADAPT-NMR

http://pine.nmrfam.wisc.edu//ADAPT-NMR

Bahrami A, Tonelli M, Sahu SC, Singarapu KK, Eghbalnia HR, et al. (2012) Robust, Integrated Computational Control of NMR Experiments to Achieve Optimal Assignment by ADAPT-NMR. PLoS ONE 7(3): e33173. doi:10.1371/journal.pone.0033173 (PLOS One link). ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) is a fully automated method for integration of protein NMR data collection, chemical shift assignment, and secondary structure determination. Lee W, Bahrami A, ...

pine.nmrfam.wisc.edu

Mani Tools - PINE Server

http://pine.nmrfam.wisc.edu//PECAN

Probabilistic secondary structure determination of protein. Hamid R. Eghbalnia, Liya Wang, Arash Bahrami, Amir Assadi, John L. Markley,. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements , Journal of Biomolecular NMR. Description of PECAN input and output files can be found below. Input file (NMRFAM-Sparky two-letter-code: n6). Output file (NDPPlot input included). Upload files to PECAN Server. Upload files to PECAN Server.

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areca.nmrfam.wisc.edu

ARECA@NMRFAM

NOESY contacts analyses ▼. Assessment of the REliability of Chemical shift Assignments) as a part of NMRFAM software packages. Uses information from the through-space internuclear proximities contained in NOE spectra of the protein. ARECA uses a truth model that indicates expectation probabilities of NOESY contacts between intra and inter-resdiue protons. These probabilities are available through our NOESY Contact Probabilities ( NCP. Chemical Shift Assignments [ instruction. 1 Select a file. The ARECA p...

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