+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>
+