<p>
The job status information will start from the "waiting in the queue to
start", then "running" and finally "postprocessing" before "done".
-Autorefresh is active every 30 sec.
+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:
</div>
</div>
-<hr>
<h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
(PDB code:1IGD) starting from the native structure</h4>
<div>
<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,
+potential energy changes, movie generated from trajectory,
+evolution of radius of gyration,
RMSD, fraction of native contacts, and CA fluctuations:
<p>
<a href="static/md1.png"><img src="static/md1.png" width="300px"></a>
only when reference structure is provided as in this example.
</div>
</div>
-<hr>
<h4><li>
Replica exchange molecular dynamics of Trp-Cage miniprotein (PDB
code:1L2Y) starting from the extended chain </h4>
<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. PDB files can be downloaded by clicking on the picture.
+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 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): minimization of 1EI0 with
-dissulfide bonds, MD simulations of 1L2Y starting from extended chain
-and multiplexed replica exchange simulations of 5G3Q:B (CASP12 target T0882)
-starting form extended chain with secondary structure restraints predicted
-by PSIPRED and Berendsen thermostat.
+in 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 selected protein (1EI0) and 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:
+<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 Trp-Cage miniprotein (PDB code:1L2Y)
+starting from 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
+<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:
+<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>
+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.
+
+ </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 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. Berendsen thermostat
+and clustering temperature 290K are selected.
+This is a full-blown structure-prediction run, but shorter
+in comparison to UNRES runs during CASP.
+
+<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>
+
+
+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.
+<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>
+<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.
+PDB files can be downloaded by clicking on the <i>Download</i> button.
+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>
<h4><li>
replica exchange molecular dynamics of
Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
<br>
-(Use <i>Load example SAXS data</i> button in advanced mode)
+(Use <i>Load example SAXS 1</i> button in advanced mode)
</h4>
<div>
<fieldset class="majorpoints">
<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 example SAXS 2</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 short (50 energy evaluations)
+initial minimization is requested.
+The SASDA25 entry of the SASBDB is used for SAXS distance distribution.
+
+<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>
+
+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.
+<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>
+<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.
+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>
+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.
+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>
projects / django_unres.git / blobdiff