1 {% extends "base.html" %}
3 {% load i18n lazysignup_tags %}
7 In order to submit a job you need to provide its name:</h4>
9 <img src="static/name.png" style="border:2px solid blueviolet">
11 UNRES server allows three types of simulations:
12 local minimization, molecular dynamics and replica exchange molecular dynamics:
14 <img src="static/types.png" style="border:2px solid blueviolet">
16 Use "Save & submit" button to start calculations.
17 <img src="static/submit.png" style="border:2px solid blueviolet">
19 Use "Refresh" button to check the status of simulation:
21 <img src="static/refresh.png" style="border:2px solid blueviolet">
24 <img src="static/done.png" style="border:2px solid blueviolet">
26 The job status information will start from the "waiting in the queue to
27 start", then "running" and finally "postprocessing" before "done".
28 Autorefresh is active every 30 sec.
30 Any single job can by accessed later using the adress of the web page
31 displayed after job submission:
32 http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
34 Registered users can save all their jobs and access them after login.
36 <h4>You can use "Load example data" button before submitting calculations
37 to try examples listed below:</h4>
40 <h4><li>Local minimization of protein A (PDB code:1BDD) structure</h4>
42 <fieldset class="majorpoints">
43 <legend class="majorpointslegend"
44 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
46 <div class="hiders" style="display:none" >
48 In this example only the PDB code of selected protein (1BDD) is provided
50 <img src="static/min.png" style="border:2px solid blueviolet">
53 The results of local minimizations show the UNRES model of 1BDD protein,
54 its total UNRES energy and overlap on starting structure:
56 <a href="static/min1.png"><img src="static/min1.png" width="300px"></a>
57 <a href="static/min2.png"><img src="static/min2.png" width="300px"></a>
59 All files generated during calculations
60 can be viewed/download by clicking on "Directory" link.
65 <h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
66 (PDB code:1IGD) starting from the native structure</h4>
68 <fieldset class="majorpoints">
69 <legend class="majorpointslegend"
70 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
72 <div class="hiders" style="display:none" >
75 <img src="static/md.png" style="border:2px solid blueviolet">
77 The results of md simulations show temperature histogram,
78 potential energy changes, evolution of radius of gyration,
79 RMSD, fraction of native contacts, and CA fluctuations:
81 <a href="static/md1.png"><img src="static/md1.png" width="300px"></a>
82 <a href="static/md2.png"><img src="static/md2.png" width="300px"></a>
83 <a href="static/md3.png"><img src="static/md3.png" width="300px"></a>
84 <a href="static/md4.png"><img src="static/md4.png" width="300px"></a>
85 <a href="static/md5.png"><img src="static/md5.png" width="300px"></a>
86 <a href="static/md6.png"><img src="static/md6.png" width="300px"></a>
87 <a href="static/md7.png"><img src="static/md7.png" width="300px"></a>
88 <a href="static/md8.png"><img src="static/md8.png" width="300px"></a>
90 Evolution of RMSD, fraction of native contacts and
91 comparison of CA fluctuations to Bfactor is presented
92 only when reference structure is provided as in this example.
97 Replica exchange molecular dynamics of Trp-Cage miniprotein (PDB
98 code:1L2Y) starting from the extended chain </h4>
100 <fieldset class="majorpoints">
101 <legend class="majorpointslegend"
102 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
104 <div class="hiders" style="display:none" >
105 <img src="static/remd.png" style="border:2px solid blueviolet">
108 Plots of histograms of UNRES energy for each temperature, and
109 energy vs temperature are presented.
110 The weighted histogram analysis (WHAM) is applied to compute the
111 probabilities of the obtained conformations to occur at particular
112 temperatures, plots of heat capacity and average RMSD as a functions
113 of temperature are shown. Replica exchanges are analyzed.
115 <a href="static/remd1.png"><img src="static/remd1.png" width="300px"></a>
116 <a href="static/remd2.png"><img src="static/remd2.png" width="300px"></a>
117 <a href="static/remd3.png"><img src="static/remd3.png" width="300px"></a>
118 <a href="static/remd4.png"><img src="static/remd4.png" width="300px"></a>
119 <a href="static/remd5.png"><img src="static/remd5.png" width="300px"></a>
120 <a href="static/remd6.png"><img src="static/remd6.png" width="300px"></a>
121 <a href="static/remd7.png"><img src="static/remd7.png" width="300px"></a>
122 <a href="static/remd8.png"><img src="static/remd8.png" width="300px"></a>
124 Finally cluster analysis is performed to select 5 families of conformations,
125 and representative model from each family is converted to all-atom
126 and refined. PDB files can be downloaded by clicking on the picture.
128 <a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>
136 Advanced mode allows for changes of more parameters of each type of
137 simulation. Separate examples are provided (use <i>Load example data</i> button as
138 in Basic mode): minimization of 1EI0 with
139 dissulfide bonds, MD simulations of 1L2Y starting from extended chain
140 and multiplexed replica exchange simulations of 5G3Q:B (CASP12 target T0882)
141 starting form extended chain with secondary structure restraints predicted
142 by PSIPRED and Berendsen thermostat.
146 Distance distribution restrained (simulated SAXS data)
147 replica exchange molecular dynamics of
148 Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
150 (Use <i>Load example SAXS data</i> button in advanced mode)
153 <fieldset class="majorpoints">
154 <legend class="majorpointslegend"
155 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
157 <div class="hiders" style="display:none" >
158 <img src="static/saxs1.png" style="border:2px solid blueviolet">
162 <img src="static/saxs2.png" style="border:2px solid blueviolet">
165 Plots of histograms of UNRES energy for each temperature, and
166 energy vs temperature are presented.
167 The weighted histogram analysis (WHAM) is applied to compute the
168 probabilities of the obtained conformations to occur at particular
169 temperatures, plots of heat capacity and average RMSD as a functions
170 of temperature are shown. Replica exchanges are analyzed.
172 <a href="static/saxs3.png"><img src="static/saxs3.png" width="300px"></a>
173 <a href="static/sasx4.png"><img src="static/saxs4.png" width="300px"></a>
174 <a href="static/saxs5.png"><img src="static/saxs5.png" width="300px"></a>
175 <a href="static/saxs6.png"><img src="static/saxs6.png" width="300px"></a>
176 <a href="static/saxs7.png"><img src="static/saxs7.png" width="300px"></a>
177 <a href="static/saxs8.png"><img src="static/saxs8.png" width="300px"></a>
178 <a href="static/saxs9.png"><img src="static/saxs9.png" width="300px"></a>
179 <a href="static/saxs10.png"><img src="static/saxs10.png" width="300px"></a>
181 Finally cluster analysis is performed to select 5 families of conformations,
182 and representative model from each family is converted to all-atom
185 <a href="static/saxs12.png"><img src="static/saxs12.png" width="300px"></a>
188 Additionaly the input reference distance distribution and
189 distance distributions for 5 final models are plotted.
191 <a href="static/saxs11.png"><img src="static/saxs11.png" width="300px"></a>
198 <script src="/static/jquery.min.js"></script>
201 $('.majorpointslegend').click(function(){
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