ARIAweb Documentation

Overview

ARIA (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation. It speeds up and automatizes the assignment process through the use of an iterative structure calculation scheme. Additionally, a refinement in explicit water improves the quality of the calculated structures, validation tests help spectroscopists to judge the quality of the final structures, and the support of the CCPN data model simplifies the exchange of information with other NMR software packages.

More information about ARIA can be found on the ARIA website.

The ARIAweb.pasteur.fr server provides access to the main ARIA software functionalities (NMR data conversion and structure calculation). In addition, structure calculation results can be easily visualised, with a dedicated molecular viewer and graphical displays of various validation statistics.

Access

Access to the ARIAweb server is free. Users are encouraged to register (Signup now button on the login page) to easily manage your ARIA projects. Use of the ARIAweb server without registration is possible as an anonymous user. Still, anonymous users have the possibility to become fully registered using Create a full account in the User menu .

Citing ARIAweb

If you use this webserver, please cite:

• Allain F, Mareuil F, Ménager H, Nilges M, Bardiaux B. ARIAweb: a server for automated NMR structure calculation. Nucleic Acids Research. 2020 Jul 2;48(W1):W41-W47. https://doi.org/10.1093/nar/gkaa362

• Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21. https://doi.org/10.1107/S0907444998003254

Projects

Calculations performed on the ARIAweb server are organized as Projects. Users can view a list of their projects or create a new project from the their homepage. To create a new projects, use the Create a new Project button on the homepage or use the button on the projects list page. On the project creation page, enter a name for your project. If you plan to use NMR data from CCPN project archive (version2 only), upload it and click the Save button. For any project, ARIAweb offers three services:

1. Data Conversion: Convert NMR data from various formats into the internal ARIA XML format.
2. Structure Calculation: Automated structure calculation from NMR data (using already converted NMR data or data from a CCPN project archive).
3. Results: Access ARIAweb results for your project (data conversion or structure calculation).

The minimal input data to perform structure calculation using NMR data with ARIAweb are:

• Sequence of the molecular chain(s) composing the molecule for which you want to calculate the structure
• One (or more) list(s) of NOE cross-peaks
• One (or more) list(s) of assigned chemical shifts

If those data are not already converted in the ARIA XML format, you have to first use the Data Conversion functionality (see below). Once the data are in the correct XML format, user can setup a new structure calculation (either by uploading XML file directly from their computer or by creating a new structure calculation from the data converted on the ARIAweb server (see below).

Alternatively, if your molecular and NMR data are already present in a CCPN project archive (version2 only) that you uploaded at the project creation, you can directly create a new structure calculation. CCPN project archive can be prepared from within CcpNmr Analysis (see the CcpNmr Analysis documentation for details).

Data Conversion

To convert molecular sequences and NMR data into the ARIA XML format (and later perform structure calculation), users must first create a new Data Conversion using the New button on the project page or use the button on the list of data conversion).

Users will be asked to enter a name for their conversion project and a name for the molecule. Next, for every chain in the molecule, use the Add a chain or button. The sequence file must be uploaded in the Input field. Accepted formats are SEQ (Xeasy 3 letters format) or PDB (Protein Data Bank). See the Example section for file format.

Similarly, users can create as many NOE Spectrum as needed using the Add a Spectrum or button. Two mandatory input files are required:

• List of assigned NMR chemical shifts (Chemicalshift input, accepted formats: XEasy, NMRview, ANSIG, Chem and Sparky).
• List of NOE cross-peaks (Crosspeaks input, accepted formats: XEasy, NMRview, ANSIG, TBL and Sparky).

Click on a format name to view an excerpt of a correctly formatted file. Input files are automatically checked for format correctness. See the Example section for example files.

When all input data have been entered, click the Finish button. You will be redirected to the list of conversions for your project. To start the data conversion process, use the Start conversion button. You will be then redirected to the Results page for your project where you can follow the status of your conversion job (see the Job status section for explanations on the different status icons). Finished jobs will be listed here. Registered users will receive a-email upon job submission with a link to the results page.

When a conversion job is finished, users can:

• Download an archive containing the converted (in ARIA XML format) data using
• Delete converted data using (This action cannot be undone!)
• Start a new structure calculation from the converted data using

Need more details on ARIA conversion ? Go the ARIA documentation.

Structure calculation

This process is identical to the use GUI of the ARIA standalone program. Users must first specified some parameters such as input data, NOE assignment criteria, number of structures to generate or parameters for the water refinement. When initiating a structure calculation from a previous conversion job on ARIAweb, mandatory input data are already pre-filled and shown next the Currently: showing the name of the file currently selected. When using data from a CCPN project, a list of possible data entries are shown for each appropriate input data type. See the Example section for file format.

The Structure Calculation form on ARIAweb is designed to guide the user through the main categories of parameters that need to be checked (if default values are used) or specified (if a user wants to change with customized values). The 4 main categories of parameters are:

1. SETUP: name of the structure calculation job and other generic info
2. DATA: all input data must be selected/uploaded here.
3. PROTOCOL: parameters related to the ARIA iterative protocols
4. STRUCTURE CALCULATION: parameters related to generation of structures with CNS

In the DATA category, accepted data format for Molecule, Cross-peaks and Chemical shifts are: XML or CCPN. See the Example section for file format. Additional input data consists in restraints files formatted in CNS TBL format (or CCPN for Hydrogen bonds, distances and dihedral angle restraints). See the Example section for file format and the CNS documentation for more details.

In each category, classes of parameters are listed on the left menu. To show the corresponding form, activate it using the slider    . The slider color code is as follows: inactive, current, validated, not validated.

By default, only basic options are displayed in each form. Enable the Expert Mode to see more options (User menu ).

To navigate between categories, use the Back or Next buttons below each form (this will validate the form and save what you have just entered). When you attain the end of the form and all categories icons are green, click the Save button. You will be redirected to the list of structure calculations for your project. To start the structure calculation process, use the Start ARIA job button. You will be then redirected to the Results page for your project where you can follow the status of your structure calculation job (see the Job status section for explanations on the different status icons). Finished jobs will be listed here. Registered users will receive a-email upon job submission with a link to the results page.

When a structure job is finished, users can:

• Download an archive containing the full ARIA run data using
• Delete the structure calculation results (This action cannot be undone!)
• Go to the visualization of the structure calculation results using

Need more details on ARIA structure calculation ? Read the ARIA documentation.

Results

As mentioned above, results for data conversion and structure calculation jobs are listed in the Results page of a project. The next figure is a screenshot of a typical Results page

The status of a job is indicated as follows:

Results archive can be downloaded using .

For structure calculation jobs, clicking the button will show the Visualisation for the job.

Visualisation

The visualisation page allows to view an analysed the results of a structure calculation job. Final structure ensemble generated by ARIAweb are displayed interactively, with various representations. Final restraints statistics, structure quality checks and bundle RMSD are shown to help the user interprets the reliability of the results. On top of that, more graphs, restraints validation and PDB files can be downloaded directly.

Click here to view a live demo of the Visualisation page for structure calculation results.

The next figure is a screenshot of a typical Visualisation page, where main components are marked in red.

Results for all ARIA iterations can be shown by selecting an iteration in the Iterations tab. The main component of the Visualisation page is the NGL viewer. By default, several representations of the structure ensemble generated by ARIA are shown:

• Sec. structure is a cartoon representation with secondary structure elements (helices and strands).
• RMS NOE viol shows side-chains colored by the average RMS (Root Mean Square) of NOE violations (per residue) from low RMS (good) to high RMS (bad) (not available for Refine iteration).
• RMSF bundle is a sausage representation with a radius proportional to the Root Mean Square Fluctuation (per residue) in the ensemble (hidden by default). More representations can be added with the add_circle_outline button.

The Representation tab (below the NGL viewer) allows to change the visibility, styling and coloring of a selected representation. By default, all structures in the bundle are shown; use the filter_frames button to select individual models for display).

The add_circle button allows to upload another PDB file to superimpose on the ARIA structure ensemble (use the layers button to superimpose an a selected structure).

Below, Restraints statistics recapitulate the number of restraints and the trend since the previous iteration for:

1. Restraints used for structure calculation (the more, the better)
2. Unsatisfied ("violated") restraints (less is better)
3. Merged (identical) restraints

The Contribution histogram gives count of restraints (from each input spectra) that have 1 (i.e. unambiguous) or more (i.e. ambiguous) assignment possibilities (or "contributions"). Ultimately, ARIA tries to reduce the ambiguity in NOE assignments, producing more unambiguous restraints. Truly ambiguous assignments can remain due to spectral overlap or chemical shifts degeneracy.

The Ensemble RMSD graph shows, for each iteration, the RMSD of the structure ensemble generated by ARIA ("bundle"), computed as the mean RMSD when superimposing of the ensemble average (after iterative superimposition). Low RMSD (< 1-2 Å) is good indicator of convergence of the NOE assignment and structure calculation process by ARIA.

The Quality checks panel summarizes the results of 3 main structural quality validators: WHAT-IF, Procheck and Molprobity. Quality scores are shown on a slider from bad to good values. Bad quality score values indicate that the input data may contain errors/inconsistencies and that ARIA was not able to produce a high quality model. We provide here some indicators on how to judge the quality checks:

1. Procheck Ramachandran percentage: for typical NMR structures deposited in the PDB, 80% of the dihedral angles lie within the preferred region of the Ramachandran plot. For high-resolution NMR structures, a higher percentage is expected (90%).

2. WHAT-IF Z-scores: WHAT-IF results are presented in the form of overall Z-scores. In general, structures with Z-scores between -2 and +2 are considered to be within a normal range and are thus good structures, while structures with Z-scores lower than -2 should be inspected further. Useful indicators of good quality are Backbone conformation and Packing quality. The bump-score also reports the number of van der Waals violations per 100 residues.

3. WHAT-IF profiles: recently, some studies have stressed that global structural indicators are not sufficient to detect errors in structures and suggested examining parameters on a per-residue basis. Such profiles for the WHAT-IF scores are produced by ARIA in the form of a PDF file. Thus, poor quality regions can be precisely identified.

4. Molprobity clashscore. this reports the number of overlaps >0.4Å per thousand atoms. For typical NMR structures deposited in the PDB, this score is generally high (>10). From our experience, the application of the log-harmonic potential along with automated weight estimation significantly improves this situation (see the More results panels).

The More results panel provides links to:

• PDB file of the structure ensemble
• graph of NOE restraints violations RMS (PDF)
• lists of NOE restraints assignments and violations (text)
• graph of WHATCHECK scores per residue (PDF, it8 and refine)
• a full ARIA run archive (ZIP)
• standard summary table of structural and restraints statistics (it8 and refine)

We invite users to read the following book chapter to learn more about ARIA and on how to judge the quality and reliability of structures determined with ARIA from NMR data.

Bardiaux B, Malliavin T, Nilges M. ARIA for solution and solid-state NMR. Methods Mol Biol. 2012;831:453-83. https://doi.org/10.1007/978-1-61779-480-3_23

Demo

In the demo, we will calculate the structure of the HRDC domain using 2 NOE crosspeaks lists.

To perform the demo:

1. Click on Create a new Project in your homepage

2. Give a name to your project (e.g. demo) and click Save

3. In the Data conversion panel, click on Demo to automatically load sample data (sequence and cross-peaks/chemical shifts lists)

4. Click on Finish to save your conversion project.

5. In the Data Conversion projects list, click on Start conversion to submit your Data Conversion job.

6. Wait until the end of the job (job status )

7. Click on to start a Structure calculation with the converted data.

8. Give a name to your Structure calculation project (e.g. demo) and click on Next

9. Click on Next until the last form, then click Save to save your Structure calculation project.

10. In the Structure Calculation projects list, click on Start ARIA job to submit your Structure Calculation.

11. Wait until the end of the job (job status )

12. When the job is finished, click on to start the job analysis and visualize the results.

Click here to view a live demo of the Visualisation page for Structure Calculation results on the HRDC domain.

Help & more

Excerpts of accepted file formats for data conversion

Example data files

ARIA documentation

Detailed documentation about the methods and usage of the ARIA software can be found on the ARIA website.

Support

We invite users to send enquiries specific to the use the ARIAweb server using the Contact form or by e-mail to ariaweb[at]pasteur.fr.

Questions about the ARIA software must be sent to the ARIA discussion group.

Limitations

• The number of simultaneous running jobs per user is 2.
• No more than 50 structures per iteration can be calculated.
• The number of MD steps in the simulated-annealing is limited to 30000 for each stage (high temperature, cooling 1 and cooling 2).
• Currently, ARIAweb only supports standard amino acid residues or DNA/RNA bases definitions and incorporation of Zinc ions in tetrahedral coordination. We recommend to use the standalone version of ARIA when modified residues or other organic ligands have to be included. See ARIA documentation for details.

Browser compatibility

Computations

ARIAweb works together with the Institut Pasteur Galaxy instance to:

1. Manage ARIA tools and workflows.
2. Run calculations on the underlying computing cluster.
3. Keep track of run status and histories.

Typical execution times for Data conversion and Structure calculation jobs are around 5 min and 90 min, respectively.

Note: Execution time of jobs submitted via ARIAweb depends on the computing cluster load and the number of Pending/Running jobs as shown on the users's homepage.

Authors

ARIAweb is developed and maintained by F. Allain, F. Mareuil, T. Huynh and B. Bardiaux from the Structural Bioinformatics Unit and Bioinformatics and Biostatistics HUB at Institut Pasteur, Paris.

The development of ARIAweb is supported by the French Institute of Bioinformatics (IFB).

ARIA is part of the ELIXIR infrastructure. ARIA is an Elixir service. Read more.

   1 124.090 0.000 N       1
   2   8.425 0.001 HN      1
   3 999.000 0.000 CA      1
   4 999.000 0.000 HA1     1
   5 999.000 0.000 HA2     1
   6 999.000 0.000 QA      1
   7 999.000 0.000 C       1
   8 118.672 0.000 N       2
   9   8.309 0.001 HN      2
  10 999.000 0.000 CA      2
          

# Number of dimensions 3
   1 119.917   8.875   8.875 2 U          2.560e+05  0.00e+00 m   0  162  163  163 0
   2 119.917   4.391   8.875 2 U          2.118e+04  0.00e+00 m   0  162  165  163 0
   3 119.917   2.051   8.875 2 U          2.822e+04  0.00e+00 m   0  162  167  163 0
          

  2.HA       4.166 0
  2.HB1      1.241 0
  3.HA2      4.178 0
  3.HA1      3.521 0
  4.HA       4.254 0
  4.HB       3.991 0
  4.HG21     0.988 0
  5.HA       5.118 0
  5.HB2      2.889 0
  5.HB1      2.413 0
  5.ND2   -104.517 0
  5.HD21     6.813 0
  5.HD22     7.189 0
  6.N       -6.486 0
          

label dataset sw sf 
H HA C13 
hhc.nv
{8000.00 } {8000.00 } {8000.00 }
{750.1071 } {750.1071 } {188.6273 }
 H.L  H.P  H.W  H.B  H.E  H.J  H.U  HA.L  HA.P  HA.W  HA.B  HA.E  HA.J  HA.U  C13.L  C13.P  C13.W  C13.B  C13.E  C13.J  C13.U  vol  int  stat  comment  flag0 
0  {59.ha}   3.863   0.039   0.039   ++   0.000   {?}   {59.hn}   7.971   0.147   0.080   ++   0.000   {?}   {59.ca}   52.865   0.459   0.247   ++   0.000   {?}  0.28357 0.28357 0 {?} 0
1  {59.HA}   3.864   0.035   0.099   ++   0.000   {?}   {59.HA}   3.867   0.081   0.186   ++   0.000   {?}   {59.CA}   52.888   0.545   1.272   ?   0.000   {?}  0.00000 5.24471 0 {?} 0
2  {59.ha 59.ha}   3.863   0.040   0.045   ++   0.000   {?}   {69.hb# 70.hb}   1.442   0.111   0.124   ++   0.000   {?}   {59.ca 59.ca}   52.908   0.560   0.627   ++   0.000   {?}  0.47090 0.47090 0 {?} 0
3  {59.ha}   3.863   0.048   0.068   ++   0.000   {?}   {59.HB#}   1.253   0.092   0.136   ++   0.000   {?}   {59.ca}   52.882   0.534   1.272   ?   0.000   {?}  0.93336 0.93336 0 {?} 0
4  {59.ha}   3.864   0.045   0.041   ++   0.000   {?}   {58.hg2#}   0.780   0.197   0.166   ++   0.000   {?}   {59.ca}   52.906   0.576   0.507   ++   0.000   {?}  0.37023 0.37023 0 {?} 0
          

ANSIG v3.3 export crosspeaks file
  1369     3
 5.854316E+01 1.369697E+00 4.041398E+00-3.353533E+07cnoe             0  2051     0     0     0  2053     0     0     0186     186 Arg     Arg CA      HA  
 5.830900E+01 8.453258E+00 3.958929E+00-4.838911E+07cnoe             0  3222  3224     0     0  3222   652     0     0139 142 139 Leu Lys Leu CA  HN  HA  
 6.019638E+01 7.830170E+00 3.824753E+00-2.420091E+07cnoe             0  3404  4493     0     0  3404  4493     0     0132 133 132 Glu Lys Glu CA  HN  HA  
 3.880658E+01 4.609407E+00 2.752022E+00-5.458084E+07cnoe             0     0   580     0   580     0     0     0  3802195 195 195 Asn Asn Asn CB  HA  HB2 
 6.213000E+01 1.915000E+00 4.301000E+00-6.447622E+07cnoe             0  2520  4233     0     0  2523  4233     0     0173 176 173 Ser Lys Ser CA  HB2 HA  
          

ANSIG v3.3 storage crosspeaks file
Nnoigen        774     3
 7.289878E+00 1.217198E+02 4.113571E+00 4.861358E+00     0     0     0     0     0     0     044  44  43  Val Val Lys HN  N   HA  
 7.286108E+00 1.217198E+02 1.908732E+00 3.746367E+00     0     0     0     0     0     0     044  44  43  Val Val Lys HN  N   HB# 
 7.755113E+00 1.157029E+02 8.016905E+00 1.914782E+00     0     0     0     0     0     0     040  40  41  Glu Glu His HN  N   HN  
 8.663352E+00 1.158256E+02 4.469307E+00 3.134771E+00     0     0     0     0     0     0     02   2   2   Ile Ile Ile HN  N   HA  
          

do ( store1 = 48.498 ) ( resid 9 and name CD )
do ( store5 = 48.498 ) ( resid 9 and name CD )
do ( store6 = 48.498 ) ( resid 9 and name CD )
do ( store1 = 61.798 ) ( resid 9 and name CA )
do ( store5 = 61.798 ) ( resid 9 and name CA )
do ( store6 = 61.798 ) ( resid 9 and name CA )
do ( store1 = 4.316 ) ( resid 9 and name HA )
do ( store5 = 4.311 ) ( resid 9 and name HA )
do ( store6 = 4.321 ) ( resid 9 and name HA )
do ( store1 = 29.646 ) ( resid 9 and name CB )
          

ASSI (( attr store1 < 2.303 and attr store1 > 2.263 )
     and bondedto ( attr store1 < 30.146 and attr store1 > 29.146 )  )
     ( attr store1 < 4.338 and attr store1 > 4.298 )
     6.0 0.1 0.1 peak 2 volume 8.214e+04 hpm1 29.646 ppm1 2.283 ppm2 4.318
ASSI (( attr store1 < 1.953 and attr store1 > 1.913 )
     and bondedto ( attr store1 < 25.787 and attr store1 > 24.787 )  )
     ( attr store1 < 2.303 and attr store1 > 2.263 )
     6.0 0.1 0.1 peak 3 volume 1.269e+05 hpm1 25.287 ppm1 1.933 ppm2 2.283
ASSI (( attr store1 < 4.414 and attr store1 > 4.374 )
     and bondedto ( attr store1 < 54.174 and attr store1 > 53.174 )  )
     ( attr store1 < 4.414 and attr store1 > 4.374 )
     6.0 0.1 0.1 peak 4 volume 2.118e+06 hpm1 53.674 ppm1 4.394 ppm2 4.394
          

 Group   Atom  Nuc    Shift   SDev  Assignments

     R2     CA  13C   56.539  0.003      3
     R2     CB  13C   30.808  0.009      3
     R2     CD  13C   43.363  0.000      1
     R2     CG  13C   27.114  0.005      2
     R2     CO  13C  176.552  0.000      1
     R2     HA   1H    4.373  0.007      2
     R2    HB#   1H    1.828  0.000      2
     R2    HD#   1H    3.172  0.000      1
     R2    HG#   1H    1.647  0.002      2
     G3     CA  13C   45.191  0.022      5
     G3     CO  13C  174.024  0.000      1
     G3    HA#   1H    3.985  0.003      3
     G3     HN   1H    8.659  0.002     17
          

      Assignment         w1         w2         w3        Volume   Data Height 

             ?-?-?      3.977     45.152      3.982   9.89e+10 lo    186256688 
     I41HD#-CD-HD#      0.818     12.622      0.820   4.10e+10 lo    116163264 
     A66HB#-CB-HB#     -0.053     15.971     -0.050   2.60e+10 lo     82174872 
             ?-?-?      1.261     52.529      4.210   2.16e+10 lo      7355818 
  K71HA-V20CG1-HG1      4.494     23.923      1.030   1.68e+10 lo      4646085 
   Q27HA-T35CG-HG#      4.492     21.361      1.393   1.60e+10 lo      3092226 
   Y26HD#-E28CA-HA      7.338     56.052      4.257   6.76e+09 lo       670847 
    W76HE3-CE3-HE3      7.491    120.787      7.492                  -26023680 
             ?-?-?      7.474     38.300      1.776                      88271 
             ?-?-?      4.643    121.824      7.008                    -114121 
             ?-?-?      1.440     29.016      1.699                   25086078