pacsy.nmrfam.wisc.edu

PACSY main page

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 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. PACSY, a relational database management system for protein structure and chemical shift analysis. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL.

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PACSY main page | pacsy.nmrfam.wisc.edu Reviews

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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 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. PACSY, a relational database management system for protein structure and chemical shift analysis. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL.

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1 introduction ▽

2 what is pacsy

3 table description

4 programs ▽

5 pacsy maker

6 pacsy analyzer

7 examples ▽

8 example of script

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introduction ▽,what is pacsy,table description,programs ▽,pacsy maker,pacsy analyzer,examples ▽,example of script,instant use,nmrfam ▽,pine server,pine sparky,lacs,adapt nmr,hifi,pecan,rna pairs,ponderosa,name,email,institution,pacsy sql,submit query

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PACSY main page | pacsy.nmrfam.wisc.edu Reviews

https://pacsy.nmrfam.wisc.edu

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 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. PACSY, a relational database management system for protein structure and chemical shift analysis. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL.

INTERNAL PAGES

pacsy.nmrfam.wisc.edu

1

PACSY introduction

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

Example of Pacsy Maker. Example of Pacsy Analyzer. PACSY (Protein structure And Chemical Shift NMR spectroscopY). Is a relational database management system that integrates information from the Protein Database Bank (PDB). The Biological Magnetic Resonance Data Bank (BMRB). And the Structural Classification of Proteins (SCOP) database. To assist in structural investigations, PACSY. Consists of seven table types. The software packages PACSY Maker. For database creation and PACSY Analyzer. Extracts and pro...

2

Instant PACSY

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

Example of Pacsy Maker. Example of Pacsy Analyzer. Using PACSY without installation. The PACSY server installed at NMRFAM is available for user requests. Users can submit an SQL sentence, and the results will be returned in the CSV file format. We strongly recommend using PACSY Analyzer. To generate the SQL sentence. When you have an SQL sentence to submit, please send an email to whlee@nmrfam.wisc.edu. You result will be sent to your email account in a couple of days. Last Updated: Mar 4, 2013.

3

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.

4

PACSY examples

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

Example of Pacsy Maker. Example of Pacsy Analyzer. Use of PACSY Maker. 1 The first thing you need to do is to download and install PACSY Maker and STRIDE ( refer to the programs tab above. 2 Make sure "stride" and "PacsyMakerQT" are executable by setting the environmental path to (link to /usr/local/bin) or something similar. Also, MySQL server program should be installed prior to DB insertion. You will see the PacsyMaker dialog if the PacsyMaker program has been installed correctly. 5 Open SCOP website.

5

PACSY programs

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

Example of Pacsy Maker. Example of Pacsy Analyzer. We provide PACSY Maker program for linux. Program is used to calculate structural attributes such as dihedral angles, secondary structures, and residue solvent accessible area; the standalone version of STRIDE must be installed before PACSY Maker is run. Hydrophobicity is calculated from the residue solvent accessible area by PACSY Maker after STRIDE analysis. Plus, Stand-alone version of MolProbity. Click to download] (Build 032814). It provides graphic...

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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.

pine.nmrfam.wisc.edu

NMRFAM Software Downloads

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

We acquire minimal information for statistics (only used in grant applications and reviews). Please fill the boxes below downloading (required)! Link to [NMRFAM Pulse Program Downloads]. Link to [NMRFAM Script Downloads]. Link to [NMRFAM Official Web Site]. Link to [NMRFAM Software Descriptions]. Please use FireFox or Google Chrome for downloading. In other way, you can just ask for a link. Varian (Agilent) - Linux. NMRFAM-SPARKY / Enhanced PyMOL / NMRmix. Ponderosa Client / Ponderosa Analyzer.

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.

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PACSY main page

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 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. PACSY, a relational database management system for protein structure and chemical shift analysis. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL.

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