In order to submit a job you need to provide its name:</h4>
<p>
<img src="static/name.png" style="border:2px solid blueviolet">
-
-UNRES server allows three types of simulations:
-local minimization, molecular dynamics, replica exchange molecular dynamics:
+<p>
+The following three types of simulations can be run with the UNRES server:
+local minimization, molecular dynamics and replica exchange molecular dynamics:
<p>
<img src="static/types.png" style="border:2px solid blueviolet">
<p>
-Use "Save & submit" button to start calculations.
+Use the "Save & submit" button to start calculations.
+<img src="static/submit.png" style="border:2px solid blueviolet">
<p>
-Use "Refresh" button to check the status of simulation:
+Use the "Refresh" button to check the status of a simulation:
<p>
<img src="static/refresh.png" style="border:2px solid blueviolet">
<p>
until
<img src="static/done.png" style="border:2px solid blueviolet">
<p>
-
-
-<h4>Use "Load example data" button before submitting calculations
-to try all examples listed below:</h4>
+After the server job has been submitted the "waiting in the queue to
+start" message will be displayed in the status field, which will subsequently change
+to "running", "postprocessing", and "done". While the job has the "running"
+status, the percentage of job accomplishment is displayed.
+It should be noted that the "100%" accomplishment refers to the production
+phase of a job, after which the postprocessing phase is triggered which also takes
+some time (up to several minutes when making a movie from an MD trajectory is
+requested) and whose progress is not monitored. The page is autorefreshed every 30 sec.
+<p>
+Any single job can by accessed later using the address of the web page
+displayed after job submission: e.g.
+http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
+<br>
+Registered users can save all their jobs and access them later after logging in.
+<p>
+<h4>You can use "Load example data" button before submitting calculations
+to try examples listed below:</h4>
<p>
<ol>
<h4><li>Local minimization of protein A (PDB code:1BDD) structure</h4>
<div class="hiders" style="display:none" >
<p>
+In this example only the PDB code of the selected protein (1BDD) is input.
+<p>
<img src="static/min.png" style="border:2px solid blueviolet">
-The results of local minimizations show the UNRES model, its total energy
-and overlap on starting structure:
+After energy minimization is accomplished, the UNRES model of the protein,
+its total UNRES energy and superposition on starting structure are displayed.
+The interactive <a href="https://github.com/arose/ngl">NGL Viewer</a> is employed, which enables the users to manipulate the structure.
<p>
<a href="static/min1.png"><img src="static/min1.png" width="300px"></a>
<a href="static/min2.png"><img src="static/min2.png" width="300px"></a>
+<p>
+All files generated during calculations
+can be viewed/download by clicking on the "Directory" link.
</div>
</div>
-<hr>
<h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
-(PDB code:1IGD) starting from the native structure</h4>
+(PDB code:1IGD) starting from the experimental structure</h4>
<div>
<fieldset class="majorpoints">
<legend class="majorpointslegend"
<p>
<img src="static/md.png" style="border:2px solid blueviolet">
<p>
-The results of md simulations show temperature histogram,
-potential energy changes, evolution of radius of gyration,
-RMSD, fraction of native contacts, and CA fluctuations:
+After the MD simulation is accomplished temperature histogram,
+plots of UNRES energy, RMSD from the experimental structure, fraction of native
+contacts, and radius of gyration vs. time, a movie of the trajectory, and
+CA-atom fluctuations are displayed.
<p>
<a href="static/md1.png"><img src="static/md1.png" width="300px"></a>
<a href="static/md2.png"><img src="static/md2.png" width="300px"></a>
<p>
Evolution of RMSD, fraction of native contacts and
comparison of CA fluctuations to Bfactor is presented
-only when reference structure is provided as in this case.
+only when the reference structure is provided, as in this example.
</div>
</div>
-<hr>
<h4><li>
-Replica exchange molecular dynamics of Trp-Cage miniprotein (PDB
+Replica exchange molecular dynamics of the Trp-Cage miniprotein (PDB
code:1L2Y) starting from the extended chain </h4>
<div>
<fieldset class="majorpoints">
<div class="hiders" style="display:none" >
<img src="static/remd.png" style="border:2px solid blueviolet">
<p>
-
-Plots of histograms of UNRES energy for each temperature, and
-energy vs temperature are presented.
-The weighted histogram analysis (WHAM) is applied to compute the
+<p>
+After a (M)REMD run is accomplished, a table showing replica-exchange statistics
+(a), plots of histograms of UNRES energy for each temperature (b), a plot of
+energy vs. temperature (c), a temperature-colored scatter plot of energy vs. RMSD
+(d), and the temperature-colored cumulative plot of rmsd vs. step number for all replicas
+(e), and a cumulative plot of walk of the replicas in temperature space (f) are
+displayed. The colors corresponding to replica temperatures are shown in panel (c),
+while different replicas are colored from black to yellow in panel (f).
+<p>
+<a href="static/remd1.png"><img src="static/remd1.png" width="300px"></a>(a)
+<a href="static/remd2.png"><img src="static/remd2.png" width="300px"></a>(b)
+<a href="static/remd3.png"><img src="static/remd3.png" width="300px"></a>(c)
+<a href="static/remd6.png"><img src="static/remd6.png" width="300px"></a>(d)
+<a href="static/remd7.png"><img src="static/remd7.png" width="300px"></a>(e)
+<a href="static/remd8.png"><img src="static/remd8.png" width="300px"></a>(f)
+<p>
+The weighted histogram analysis method (WHAM) is applied to compute the
probabilities of the obtained conformations to occur at particular
-temperatures, plots of heat capacity and average RMSD as a functions
-of temperature are shown. Replica exchanges are analyzed.
-<p>
-<a href="static/remd1.png"><img src="static/remd1.png" width="300px"></a>
-<a href="static/remd2.png"><img src="static/remd2.png" width="300px"></a>
-<a href="static/remd3.png"><img src="static/remd3.png" width="300px"></a>
-<a href="static/remd4.png"><img src="static/remd4.png" width="300px"></a>
-<a href="static/remd5.png"><img src="static/remd5.png" width="300px"></a>
-<a href="static/remd6.png"><img src="static/remd6.png" width="300px"></a>
-<a href="static/remd7.png"><img src="static/remd7.png" width="300px"></a>
-<a href="static/remd8.png"><img src="static/remd8.png" width="300px"></a>
+temperatures and, consequently, the plots of heat capacity (g) and ensemble-averaged RMSD (h) as a functions
+of temperature; these are shown in the respective graphs.
+<p>
+<a href="static/remd4.png"><img src="static/remd4.png" width="300px"></a>(g)
+<a href="static/remd5.png"><img src="static/remd5.png" width="300px"></a>(h)
+<p>
+Note! Panels are labeled in this tutorial only and labels are not displayed
+in the outputs from real server jobs.
<p>
Finally cluster analysis is performed to select 5 families of conformations,
and representative model from each family is converted to all-atom
-and refined.
+and refined. Models are shown using NGL Viewer.
+PDB files can be downloaded by clicking on the <i>Download</i> button.
<p>
<a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>
</div>
</div>
+</ol>
+<hr>
+Advanced mode enables the user to change more parameters for each type of
+simulation. Separate examples are provided (use the <i>Load example data</i> button as
+in the Basic mode):
+<ol>
+<h4><li>
+Minimization of the P8MTCP1 disulfide-bonded helical hairpin miniprotein
+(PDB code: 1EI0).</h4>
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+<p>
+In this example the PDB code of the selected protein (1EI0) and the OPT-WTFSA-2
+force field are selected:
+<p>
+<img src="static/min_adv.png" style="border:2px solid blueviolet">
+
+After the minimization is accomplished, the UNRES model of 1EI0 protein
+with two disulfide bonds as read from the respective PDB file,
+its total UNRES energy and superposition on the starting structure are displayed:
+<p>
+<a href="static/min_adv1.png"><img src="static/min_adv1.png" width="300px"></a>
+<a href="static/min_adv2.png"><img src="static/min_adv2.png" width="300px"></a>
+<a href="static/min_adv3.png"><img src="static/min_adv3.png" width="300px"></a>
+
+ </div>
+</div>
+
+<h4><li>
+Canonical MD simulations of the Trp-Cage miniprotein (PDB code:1L2Y)
+starting from the extended chain.</h4>
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+In this example the PDB code of the selected protein (1L2Y) and
+option to write trajectory as a PDB file are selected, saving trajectory
+as a PDB file allows its 3D visualisation by NGL Viewer in addition to
+the movie which is always generated from the MD trajectory
+<p>
+<img src="static/md_adv.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/md_adv0.png" style="border:2px solid blueviolet">
+<p>
+After the MD simulation is accomplished temperature histogram,
+plots of UNRES energy, RMSD from the experimental structure, fraction of native
+contacts, and radius of gyration vs. time, and a movie of the trajectory are displayed.
+<p>
+<a href="static/md_adv1.png"><img src="static/md_adv1.png" width="300px"></a>
+<a href="static/md_adv2.png"><img src="static/md_adv2.png" width="300px"></a>
+<a href="static/md_adv3.png"><img src="static/md_adv3.png" width="300px"></a>
+<a href="static/md_adv4.png"><img src="static/md_adv4.png" width="300px"></a>
+<a href="static/md_adv5.png"><img src="static/md_adv5.png" width="300px"></a>
+<a href="static/md_adv6.png"><img src="static/md_adv6.png" width="300px"></a>
+<a href="static/md_adv7.png"><img src="static/md_adv7.png" width="300px"></a>
+<p>
+The CA fluctuations are not analyzed for start from the extended structure
+because of large scale conformational changes during folding.
+
+ </div>
+</div>
+
+
+<h4><li>
+MREMD simulations of 5G3Q:B (CASP12 target T0882)</h4>
+
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+This simulation starts from the extended chain, 2000000 steps for each of 16
+replicas (8 temperatures with multiplexing 2)
+are run and secondary-structure restraints predicted by PSIPRED and
+obtained at the CASP12 time when the experimental 5G3Q structure
+was not included in the PDB database are used. The Berendsen thermostat
+was employed and the resulting conformational ensemble was clustered
+at the temperature of 290K.
+This is a full-blown structure-prediction run, but shorter
+compared to the UNRES runs during the CASP exercises.
+
+<p>
+<img src="static/remd_adv.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/remd_adv01.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/remd_adv02.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/remd_adv03.png" style="border:2px solid blueviolet">
+<p>
+
+
+The output items are the same as those discussed with the Basic mode Example 3.
+<p>
+<a href="static/remd_adv1.png"><img src="static/remd_adv1.png" width="300px"></a>
+<a href="static/remd_adv2.png"><img src="static/remd_adv2.png" width="300px"></a>
+<a href="static/remd_adv3.png"><img src="static/remd_adv3.png" width="300px"></a>
+<a href="static/remd_adv6.png"><img src="static/remd_adv6.png" width="300px"></a>
+<a href="static/remd_adv7.png"><img src="static/remd_adv7.png" width="300px"></a>
+<a href="static/remd_adv8.png"><img src="static/remd_adv8.png" width="300px"></a>
+<a href="static/remd_adv4.png"><img src="static/remd_adv4.png" width="300px"></a>
+<a href="static/remd_adv5.png"><img src="static/remd_adv5.png" width="300px"></a>
+<p>
+The final models are shown using NGL Viewer.
+PDB files can be downloaded by clicking on the <i>Download</i> button.
+The RMSD of model 1
+from the experimental structure is 3.6 A and
+the GDT_TS is 58.8 %
+
+<p>
+<a href="static/remd_adv9.png"><img src="static/remd_adv9.png" width="300px"></a>
+
+<p>
+
+
+ </div>
+</div>
+
+
<hr>
-Advanced mode allows for changes of more parameters of each type of
-simulation. Separate examples are provided: minimization of 1EI0 with
-dissulfide bonds, MD simulations of 1L2Y starting from extended chain
-and replica exchange simulations of 1E0G starting form extended chain
-using new UNRES force field and Berendsen thermostat.
+<h4><li>
+Distance distribution restrained (simulated SAXS data)
+replica exchange molecular dynamics of
+Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
+<br>
+(Use <i>Load SAXS 1 example</i> button in advanced mode)
+</h4>
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+<img src="static/saxs1.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/saxs2.png" style="border:2px solid blueviolet">
+<p>
+
+The output items are the same as those displayed with the Basic mode example 3.
+Additionaly the input reference distance distribution and
+distance distributions for 5 final models are plotted.
+<p>
+<a href="static/saxs3.png"><img src="static/saxs3.png" width="300px"></a>
+<a href="static/sasx4.png"><img src="static/saxs4.png" width="300px"></a>
+<a href="static/saxs5.png"><img src="static/saxs5.png" width="300px"></a>
+<a href="static/saxs8.png"><img src="static/saxs8.png" width="300px"></a>
+<a href="static/saxs9.png"><img src="static/saxs9.png" width="300px"></a>
+<a href="static/saxs10.png"><img src="static/saxs10.png" width="300px"></a>
+<a href="static/saxs6.png"><img src="static/saxs6.png" width="300px"></a>
+<a href="static/saxs7.png"><img src="static/saxs7.png" width="300px"></a>
+<p>
+Finally models.
+<p>
+<a href="static/saxs12.png"><img src="static/saxs12.png" width="300px"></a>
+<p>
+Comparison of the input distance distributions with those calculated from the 5 models.
+<p>
+<a href="static/saxs11.png"><img src="static/saxs11.png" width="300px"></a>
+
+</div>
+</div>
+
+<h4><li>
+Distance distribution restrained (real SAXS data)
+replica exchange molecular dynamics of
+the central portion of Factor H (PDB code:2KMS).
+<br>
+(Use <i>Load SAXS 2 example</i> button in advanced mode)
+</h4>
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+REMD simulation starts from the experimental NMR structure. Secondary
+structure restraints are used. Only a short (50 energy evaluations)
+initial minimization is requested.
+The distance distribution has been downloaded from the SASBDB database (the SASDA25 entry).
+
+<img src="static/saxs2_1.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/saxs2_2.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/saxs2_3.png" style="border:2px solid blueviolet">
+
+<p>
+
+The input items are the same as those in the Advanced mode Example 2.
+<p>
+<a href="static/sasx2_4.png"><img src="static/saxs2_4.png" width="300px"></a>
+<a href="static/saxs2_5.png"><img src="static/saxs2_5.png" width="300px"></a>
+<a href="static/saxs2_6.png"><img src="static/saxs2_6.png" width="300px"></a>
+<a href="static/saxs2_9.png"><img src="static/saxs2_9.png" width="300px"></a>
+<a href="static/saxs2_10.png"><img src="static/saxs2_10.png" width="300px"></a>
+<a href="static/saxs2_11.png"><img src="static/saxs2_11.png" width="300px"></a>
+<a href="static/saxs2_7.png"><img src="static/saxs2_7.png" width="300px"></a>
+<a href="static/saxs2_8.png"><img src="static/saxs2_8.png" width="300px"></a>
+<p>
+Final models.
+In the UNRES calculated
+structures, the domains are at a larger angle than
+those in the experimental NMR structure.
+
+<p>
+<a href="static/saxs2_13.png"><img src="static/saxs2_13.png" width="300px"></a>
+
+<p>
+Comparison of the input distance distributions with those calculated from the 5 models.
+Much better agreement, in
+particular in the long-distance part is obtained
+for structres from the UNRES simulation.
+<p>
+<a href="static/saxs2_12.png"><img src="static/saxs2_12.png" width="300px"></a>
+
+
+</div>
+
+</div>
+
<script src="/static/jquery.min.js"></script>
<script>
-$('.majorpoints').click(function(){
- $(this).find('.hiders').toggle();
- if($(this).find('.majorpointslegend').text()=='Show'){
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+ $(this.parentNode).find('.hiders').toggle();
+ if($(this.parentNode).find('.majorpointslegend').text()=='Show'){
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-{% endblock %}
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+{% endblock %}
projects / django_unres.git / blobdiff