<p>
<img src="static/name.png" style="border:2px solid blueviolet">
<p>
-UNRES server allows three types of simulations:
+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>
-The job status information will start from the "waiting in the queue to
-start", then "running" and finally "postprocessing" before "done".
-Postprocessing do not count to 100%. Autorefresh is active every 30 sec.
-<p>
-Any single job can by accessed later using the adress of the web page
-displayed after job submission:
+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 after login.
+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>
<div class="hiders" style="display:none" >
<p>
-In this example only the PDB code of selected protein (1BDD) is provided
+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 of 1BDD protein,
-its total UNRES 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 "Directory" link.
+can be viewed/download by clicking on the "Directory" link.
</div>
</div>
<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, movie generated from trajectory,
-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 example.
+only when the reference structure is provided, as in this example.
</div>
</div>
<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
</div>
</ol>
<hr>
-Advanced mode allows for changes of more parameters of each type of
-simulation. Separate examples are provided (use <i>Load example data</i> button as
-in Basic mode):
+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
<div class="hiders" style="display:none" >
<p>
-In this example the PDB code of selected protein (1EI0) and opt-wtfsa-2
+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">
-The results of local minimizations show the UNRES model of 1EI0 protein
-with two dissulfide bonds as read from pdb,
-its total UNRES energy and overlap on starting structure:
+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>
</div>
<h4><li>
-Canonical MD simulations of Trp-Cage miniprotein (PDB code:1L2Y)
-starting from extended chain.</h4>
+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 selected protein (1L2Y) and
-option to write trajectory as pdb are selected, saving trajectory
-as pdb allows its 3D visualisation in NGL Viewer in addtion to
-movie which is always generated from the MD trajectory
+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>
-The results of md simulations show temperature histogram,
-potential energy changes, movie generated from trajectory,
-trajectory visualization in NGL Viewer,
-evolution of radius of gyration,
-RMSD, fraction of native contacts:
+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_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>
-Evolution of RMSD and fraction of native contacts
-is shown only when reference structure is provided as in this example.
The CA fluctuations are not analyzed for start from the extended structure
because of large scale conformational changes during folding.
style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
<div class="hiders" style="display:none" >
-This simulation starts from extended chain, 2000000 steps for each of 16
+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
+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. Berendsen thermostat
-and clustering temperature 290K are selected.
+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
-in comparison to UNRES runs during CASP.
+compared to the UNRES runs during the CASP exercises.
<p>
<img src="static/remd_adv.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
-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.
+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_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>
<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>
-Finally cluster analysis is performed to select 5 families of conformations,
-and representative model from each family is converted to all-atom
-and refined. Models are shown using NGL Viewer.
+The final models are shown using NGL Viewer.
PDB files can be downloaded by clicking on the <i>Download</i> button.
-RMSD of model 1
+The RMSD of model 1
from the experimental structure is 3.6 A and
-the GDT TS is 58.8 %
+the GDT_TS is 58.8 %
<p>
<a href="static/remd_adv9.png"><img src="static/remd_adv9.png" width="300px"></a>
replica exchange molecular dynamics of
Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
<br>
-(Use <i>Load example SAXS 1</i> button in advanced mode)
+(Use <i>Load SAXS 1 example</i> button in advanced mode)
</h4>
<div>
<fieldset class="majorpoints">
<img src="static/saxs2.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
-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.
+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/saxs6.png"><img src="static/saxs6.png" width="300px"></a>
-<a href="static/saxs7.png"><img src="static/saxs7.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 cluster analysis is performed to select 5 families of conformations,
-and representative model from each family is converted to all-atom
-and refined.
+Finally models.
<p>
<a href="static/saxs12.png"><img src="static/saxs12.png" width="300px"></a>
-
<p>
-Additionaly the input reference distance distribution and
-distance distributions for 5 final models are plotted.
+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>
replica exchange molecular dynamics of
the central portion of Factor H (PDB code:2KMS).
<br>
-(Use <i>Load example SAXS 2</i> button in advanced mode)
+(Use <i>Load SAXS 2 example</i> button in advanced mode)
</h4>
<div>
<fieldset class="majorpoints">
<div class="hiders" style="display:none" >
REMD simulation starts from the experimental NMR structure. Secondary
-structure restraints are used. Only short (50 energy evaluations)
+structure restraints are used. Only a short (50 energy evaluations)
initial minimization is requested.
-The SASDA25 entry of the SASBDB is used for SAXS distance distribution.
+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>
<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
-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.
+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_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>
<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>
-Finally cluster analysis is performed to select 5 families of conformations,
-and representative model from each family is converted to all-atom
-and refined.
+Final models.
In the UNRES calculated
structures, the domains are at a larger angle than
those in the experimental NMR structure.
<a href="static/saxs2_13.png"><img src="static/saxs2_13.png" width="300px"></a>
<p>
-Additionaly the input reference distance distribution and
-distance distributions for 5 final models are plotted.
-The distance distribution calculated from the
-experimental NMR structure does not fully overlap with that from
-SAXS; in particular, the plot calculated from the 2KMS
-structure decays to 0 quicker than that from SAXS.
+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.
</script>
-{% endblock %}
\ No newline at end of file
+{% endblock %}
projects / django_unres.git / commitdiff