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".
29 Any single job can by accessed later using the adress of the web page
30 displayed after job submission:
31 http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
33 Registered users can save all their jobs and access them after login.
35 <h4>You can use "Load example data" button before submitting calculations
36 to try examples listed below:</h4>
39 <h4><li>Local minimization of protein A (PDB code:1BDD) structure</h4>
41 <fieldset class="majorpoints">
42 <legend class="majorpointslegend"
43 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
45 <div class="hiders" style="display:none" >
47 In this example only the PDB code of selected protein (1BDD) is provided
49 <img src="static/min.png" style="border:2px solid blueviolet">
52 The results of local minimizations show the UNRES model of 1BDD protein,
53 its total UNRES energy and overlap on starting structure:
55 <a href="static/min1.png"><img src="static/min1.png" width="300px"></a>
56 <a href="static/min2.png"><img src="static/min2.png" width="300px"></a>
58 All files generated during calculations
59 can be viewed/download by clicking on "Directory" link.
64 <h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
65 (PDB code:1IGD) starting from the native structure</h4>
67 <fieldset class="majorpoints">
68 <legend class="majorpointslegend"
69 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
71 <div class="hiders" style="display:none" >
74 <img src="static/md.png" style="border:2px solid blueviolet">
76 The results of md simulations show temperature histogram,
77 potential energy changes, evolution of radius of gyration,
78 RMSD, fraction of native contacts, and CA fluctuations:
80 <a href="static/md1.png"><img src="static/md1.png" width="300px"></a>
81 <a href="static/md2.png"><img src="static/md2.png" width="300px"></a>
82 <a href="static/md3.png"><img src="static/md3.png" width="300px"></a>
83 <a href="static/md4.png"><img src="static/md4.png" width="300px"></a>
84 <a href="static/md5.png"><img src="static/md5.png" width="300px"></a>
85 <a href="static/md6.png"><img src="static/md6.png" width="300px"></a>
86 <a href="static/md7.png"><img src="static/md7.png" width="300px"></a>
87 <a href="static/md8.png"><img src="static/md8.png" width="300px"></a>
89 Evolution of RMSD, fraction of native contacts and
90 comparison of CA fluctuations to Bfactor is presented
91 only when reference structure is provided as in this example.
96 Replica exchange molecular dynamics of Trp-Cage miniprotein (PDB
97 code:1L2Y) starting from the extended chain </h4>
99 <fieldset class="majorpoints">
100 <legend class="majorpointslegend"
101 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
103 <div class="hiders" style="display:none" >
104 <img src="static/remd.png" style="border:2px solid blueviolet">
107 Plots of histograms of UNRES energy for each temperature, and
108 energy vs temperature are presented.
109 The weighted histogram analysis (WHAM) is applied to compute the
110 probabilities of the obtained conformations to occur at particular
111 temperatures, plots of heat capacity and average RMSD as a functions
112 of temperature are shown. Replica exchanges are analyzed.
114 <a href="static/remd1.png"><img src="static/remd1.png" width="300px"></a>
115 <a href="static/remd2.png"><img src="static/remd2.png" width="300px"></a>
116 <a href="static/remd3.png"><img src="static/remd3.png" width="300px"></a>
117 <a href="static/remd4.png"><img src="static/remd4.png" width="300px"></a>
118 <a href="static/remd5.png"><img src="static/remd5.png" width="300px"></a>
119 <a href="static/remd6.png"><img src="static/remd6.png" width="300px"></a>
120 <a href="static/remd7.png"><img src="static/remd7.png" width="300px"></a>
121 <a href="static/remd8.png"><img src="static/remd8.png" width="300px"></a>
123 Finally cluster analysis is performed to select 5 families of conformations,
124 and representative model from each family is converted to all-atom
125 and refined. PDB files can be downloaded by clicking on the picture.
127 <a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>
135 Advanced mode allows for changes of more parameters of each type of
136 simulation. Separate examples are provided: minimization of 1EI0 with
137 dissulfide bonds, MD simulations of 1L2Y starting from extended chain
138 and replica exchange simulations of 1E0G starting form extended chain
139 using new UNRES force field and Berendsen thermostat.
143 Distance distribution restrained (simulated SAXS data)
144 replica exchange molecular dynamics of
145 Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
147 (Use <i>Load example SAXS data</i> button in advanced mode)
150 <fieldset class="majorpoints">
151 <legend class="majorpointslegend"
152 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
154 <div class="hiders" style="display:none" >
155 <img src="static/saxs1.png" style="border:2px solid blueviolet">
159 <img src="static/saxs2.png" style="border:2px solid blueviolet">
162 Plots of histograms of UNRES energy for each temperature, and
163 energy vs temperature are presented.
164 The weighted histogram analysis (WHAM) is applied to compute the
165 probabilities of the obtained conformations to occur at particular
166 temperatures, plots of heat capacity and average RMSD as a functions
167 of temperature are shown. Replica exchanges are analyzed.
169 <a href="static/saxs3.png"><img src="static/saxs3.png" width="300px"></a>
170 <a href="static/sasx4.png"><img src="static/saxs4.png" width="300px"></a>
171 <a href="static/saxs5.png"><img src="static/saxs5.png" width="300px"></a>
172 <a href="static/saxs6.png"><img src="static/saxs6.png" width="300px"></a>
173 <a href="static/saxs7.png"><img src="static/saxs7.png" width="300px"></a>
174 <a href="static/saxs8.png"><img src="static/saxs8.png" width="300px"></a>
175 <a href="static/saxs9.png"><img src="static/saxs9.png" width="300px"></a>
176 <a href="static/saxs10.png"><img src="static/saxs10.png" width="300px"></a>
178 Finally cluster analysis is performed to select 5 families of conformations,
179 and representative model from each family is converted to all-atom
182 <a href="static/saxs12.png"><img src="static/saxs12.png" width="300px"></a>
185 Additionaly the input reference distance distribution and
186 distance distributions for 5 final models are plotted.
188 <a href="static/saxs11.png"><img src="static/saxs11.png" width="300px"></a>
195 <script src="/static/jquery.min.js"></script>
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