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 The following three types of simulations can be run with the UNRES server:
12 local minimization, molecular dynamics and replica exchange molecular dynamics:
14 <img src="static/types.png" style="border:2px solid blueviolet">
16 Use the "Save & submit" button to start calculations.
17 <img src="static/submit.png" style="border:2px solid blueviolet">
19 Use the "Refresh" button to check the status of a simulation:
21 <img src="static/refresh.png" style="border:2px solid blueviolet">
24 <img src="static/done.png" style="border:2px solid blueviolet">
26 After the server job has been submitted the "waiting in the queue to
27 start" message will be displayed in the status field, which will subsequently change
28 to "running", "postprocessing", and "done". While the job has the "running"
29 status, the percentage of job accomplishment is displayed.
30 It should be noted that the "100%" accomplishment refers to the production
31 phase of a job, after which the postprocessing phase is triggered which also takes
32 some time (up to several minutes when making a movie from an MD trajectory is
33 requested) and whose progress is not monitored. The page is autorefreshed every 30 sec.
35 Any single job can by accessed later using the address of the web page
36 displayed after job submission: e.g.
37 http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
39 Registered users can save all their jobs and access them later after logging in.
41 <h4>You can use "Load example data" button before submitting calculations
42 to try examples listed below:</h4>
45 <h4><li>Local minimization of protein A (PDB code:1BDD) structure</h4>
47 <fieldset class="majorpoints">
48 <legend class="majorpointslegend"
49 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
51 <div class="hiders" style="display:none" >
53 In this example only the PDB code of the selected protein (1BDD) is input.
55 <img src="static/min.png" style="border:2px solid blueviolet">
58 After energy minimization is accomplished, the UNRES model of the protein,
59 its total UNRES energy and superposition on starting structure are displayed.
60 The interactive <a href="https://github.com/arose/ngl">NGL Viewer</a> is employed, which enables the users to manipulate the structure.
62 <a href="static/min1.png"><img src="static/min1.png" width="300px"></a>
63 <a href="static/min2.png"><img src="static/min2.png" width="300px"></a>
65 All files generated during calculations
66 can be viewed/download by clicking on the "Directory" link.
70 <h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
71 (PDB code:1IGD) starting from the experimental structure</h4>
73 <fieldset class="majorpoints">
74 <legend class="majorpointslegend"
75 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
77 <div class="hiders" style="display:none" >
80 <img src="static/md.png" style="border:2px solid blueviolet">
82 After the MD simulation is accomplished temperature histogram,
83 plots of UNRES energy, RMSD from the experimental structure, fraction of native
84 contacts, and radius of gyration vs. time, a movie of the trajectory, and
85 CA-atom fluctuations are displayed.
87 <a href="static/md1.png"><img src="static/md1.png" width="300px"></a>
88 <a href="static/md2.png"><img src="static/md2.png" width="300px"></a>
89 <a href="static/md3.png"><img src="static/md3.png" width="300px"></a>
90 <a href="static/md4.png"><img src="static/md4.png" width="300px"></a>
91 <a href="static/md5.png"><img src="static/md5.png" width="300px"></a>
92 <a href="static/md6.png"><img src="static/md6.png" width="300px"></a>
93 <a href="static/md7.png"><img src="static/md7.png" width="300px"></a>
94 <a href="static/md8.png"><img src="static/md8.png" width="300px"></a>
96 Evolution of RMSD, fraction of native contacts and
97 comparison of CA fluctuations to Bfactor is presented
98 only when the reference structure is provided, as in this example.
102 Replica exchange molecular dynamics of the Trp-Cage miniprotein (PDB
103 code:1L2Y) starting from the extended chain </h4>
105 <fieldset class="majorpoints">
106 <legend class="majorpointslegend"
107 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
109 <div class="hiders" style="display:none" >
110 <img src="static/remd.png" style="border:2px solid blueviolet">
113 After a (M)REMD run is accomplished, a table showing replica-exchange statistics
114 (a), plots of histograms of UNRES energy for each temperature (b), a plot of
115 energy vs. temperature (c), a temperature-colored scatter plot of energy vs. RMSD
116 (d), and the temperature-colored cumulative plot of rmsd vs. step number for all replicas
117 (e), and a cumulative plot of walk of the replicas in temperature space (f) are
118 displayed. The colors corresponding to replica temperatures are shown in panel (c),
119 while different replicas are colored from black to yellow in panel (f).
121 <a href="static/remd1.png"><img src="static/remd1.png" width="300px"></a>(a)
122 <a href="static/remd2.png"><img src="static/remd2.png" width="300px"></a>(b)
123 <a href="static/remd3.png"><img src="static/remd3.png" width="300px"></a>(c)
124 <a href="static/remd6.png"><img src="static/remd6.png" width="300px"></a>(d)
125 <a href="static/remd7.png"><img src="static/remd7.png" width="300px"></a>(e)
126 <a href="static/remd8.png"><img src="static/remd8.png" width="300px"></a>(f)
128 The weighted histogram analysis method (WHAM) is applied to compute the
129 probabilities of the obtained conformations to occur at particular
130 temperatures and, consequently, the plots of heat capacity (g) and ensemble-averaged RMSD (h) as a functions
131 of temperature; these are shown in the respective graphs.
133 <a href="static/remd4.png"><img src="static/remd4.png" width="300px"></a>(g)
134 <a href="static/remd5.png"><img src="static/remd5.png" width="300px"></a>(h)
136 Note! Panels are labeled in this tutorial only and labels are not displayed
137 in the outputs from real server jobs.
139 Finally cluster analysis is performed to select 5 families of conformations,
140 and representative model from each family is converted to all-atom
141 and refined. Models are shown using NGL Viewer.
142 PDB files can be downloaded by clicking on the <i>Download</i> button.
144 <a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>
153 Advanced mode enables the user to change more parameters for each type of
154 simulation. Separate examples are provided (use the <i>Load example data</i> button as
158 Minimization of the P8MTCP1 disulfide-bonded helical hairpin miniprotein
159 (PDB code: 1EI0).</h4>
161 <fieldset class="majorpoints">
162 <legend class="majorpointslegend"
163 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
165 <div class="hiders" style="display:none" >
167 In this example the PDB code of the selected protein (1EI0) and the OPT-WTFSA-2
168 force field are selected:
170 <img src="static/min_adv.png" style="border:2px solid blueviolet">
172 After the minimization is accomplished, the UNRES model of 1EI0 protein
173 with two disulfide bonds as read from the respective PDB file,
174 its total UNRES energy and superposition on the starting structure are displayed:
176 <a href="static/min_adv1.png"><img src="static/min_adv1.png" width="300px"></a>
177 <a href="static/min_adv2.png"><img src="static/min_adv2.png" width="300px"></a>
178 <a href="static/min_adv3.png"><img src="static/min_adv3.png" width="300px"></a>
184 Canonical MD simulations of the Trp-Cage miniprotein (PDB code:1L2Y)
185 starting from the extended chain.</h4>
187 <fieldset class="majorpoints">
188 <legend class="majorpointslegend"
189 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
191 <div class="hiders" style="display:none" >
192 In this example the PDB code of the selected protein (1L2Y) and
193 option to write trajectory as a PDB file are selected, saving trajectory
194 as a PDB file allows its 3D visualisation by NGL Viewer in addition to
195 the movie which is always generated from the MD trajectory
197 <img src="static/md_adv.png" style="border:2px solid blueviolet">
201 <img src="static/md_adv0.png" style="border:2px solid blueviolet">
203 After the MD simulation is accomplished temperature histogram,
204 plots of UNRES energy, RMSD from the experimental structure, fraction of native
205 contacts, and radius of gyration vs. time, and a movie of the trajectory are displayed.
207 <a href="static/md_adv1.png"><img src="static/md_adv1.png" width="300px"></a>
208 <a href="static/md_adv2.png"><img src="static/md_adv2.png" width="300px"></a>
209 <a href="static/md_adv3.png"><img src="static/md_adv3.png" width="300px"></a>
210 <a href="static/md_adv4.png"><img src="static/md_adv4.png" width="300px"></a>
211 <a href="static/md_adv5.png"><img src="static/md_adv5.png" width="300px"></a>
212 <a href="static/md_adv6.png"><img src="static/md_adv6.png" width="300px"></a>
213 <a href="static/md_adv7.png"><img src="static/md_adv7.png" width="300px"></a>
215 The CA fluctuations are not analyzed for start from the extended structure
216 because of large scale conformational changes during folding.
223 MREMD simulations of 5G3Q:B (CASP12 target T0882)</h4>
226 <fieldset class="majorpoints">
227 <legend class="majorpointslegend"
228 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
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231 This simulation starts from the extended chain, 2000000 steps for each of 16
232 replicas (8 temperatures with multiplexing 2)
233 are run and secondary-structure restraints predicted by PSIPRED and
234 obtained at the CASP12 time when the experimental 5G3Q structure
235 was not included in the PDB database are used. The Berendsen thermostat
236 was employed and the resulting conformational ensemble was clustered
237 at the temperature of 290K.
238 This is a full-blown structure-prediction run, but shorter
239 compared to the UNRES runs during the CASP exercises.
242 <img src="static/remd_adv.png" style="border:2px solid blueviolet">
246 <img src="static/remd_adv01.png" style="border:2px solid blueviolet">
250 <img src="static/remd_adv02.png" style="border:2px solid blueviolet">
254 <img src="static/remd_adv03.png" style="border:2px solid blueviolet">
258 The output items are the same as those discussed with the Basic mode Example 3.
260 <a href="static/remd_adv1.png"><img src="static/remd_adv1.png" width="300px"></a>
261 <a href="static/remd_adv2.png"><img src="static/remd_adv2.png" width="300px"></a>
262 <a href="static/remd_adv3.png"><img src="static/remd_adv3.png" width="300px"></a>
263 <a href="static/remd_adv6.png"><img src="static/remd_adv6.png" width="300px"></a>
264 <a href="static/remd_adv7.png"><img src="static/remd_adv7.png" width="300px"></a>
265 <a href="static/remd_adv8.png"><img src="static/remd_adv8.png" width="300px"></a>
266 <a href="static/remd_adv4.png"><img src="static/remd_adv4.png" width="300px"></a>
267 <a href="static/remd_adv5.png"><img src="static/remd_adv5.png" width="300px"></a>
269 The final models are shown using NGL Viewer.
270 PDB files can be downloaded by clicking on the <i>Download</i> button.
272 from the experimental structure is 3.6 A and
276 <a href="static/remd_adv9.png"><img src="static/remd_adv9.png" width="300px"></a>
287 Distance distribution restrained (simulated SAXS data)
288 replica exchange molecular dynamics of
289 Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
291 (Use <i>Load SAXS 1 example</i> button in advanced mode)
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299 <img src="static/saxs1.png" style="border:2px solid blueviolet">
303 <img src="static/saxs2.png" style="border:2px solid blueviolet">
306 The output items are the same as those displayed with the Basic mode example 3.
307 Additionaly the input reference distance distribution and
308 distance distributions for 5 final models are plotted.
310 <a href="static/saxs3.png"><img src="static/saxs3.png" width="300px"></a>
311 <a href="static/sasx4.png"><img src="static/saxs4.png" width="300px"></a>
312 <a href="static/saxs5.png"><img src="static/saxs5.png" width="300px"></a>
313 <a href="static/saxs8.png"><img src="static/saxs8.png" width="300px"></a>
314 <a href="static/saxs9.png"><img src="static/saxs9.png" width="300px"></a>
315 <a href="static/saxs10.png"><img src="static/saxs10.png" width="300px"></a>
316 <a href="static/saxs6.png"><img src="static/saxs6.png" width="300px"></a>
317 <a href="static/saxs7.png"><img src="static/saxs7.png" width="300px"></a>
321 <a href="static/saxs12.png"><img src="static/saxs12.png" width="300px"></a>
323 Comparison of the input distance distributions with those calculated from the 5 models.
325 <a href="static/saxs11.png"><img src="static/saxs11.png" width="300px"></a>
331 Distance distribution restrained (real SAXS data)
332 replica exchange molecular dynamics of
333 the central portion of Factor H (PDB code:2KMS).
335 (Use <i>Load SAXS 2 example</i> button in advanced mode)
338 <fieldset class="majorpoints">
339 <legend class="majorpointslegend"
340 style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
342 <div class="hiders" style="display:none" >
343 REMD simulation starts from the experimental NMR structure (the first model
344 is taken as the input structure). Secondary
345 structure restraints are used. Only a short (50 energy evaluations)
346 initial minimization is requested.
347 The distance distribution has been downloaded from the SASBDB database (the SASDA25 entry).
349 <img src="static/saxs2_1.png" style="border:2px solid blueviolet">
353 <img src="static/saxs2_2.png" style="border:2px solid blueviolet">
357 <img src="static/saxs2_3.png" style="border:2px solid blueviolet">
361 The input items are the same as those in the Advanced mode Example 2.
363 <a href="static/sasx2_4.png"><img src="static/saxs2_4.png" width="300px"></a>
364 <a href="static/saxs2_5.png"><img src="static/saxs2_5.png" width="300px"></a>
365 <a href="static/saxs2_6.png"><img src="static/saxs2_6.png" width="300px"></a>
366 <a href="static/saxs2_9.png"><img src="static/saxs2_9.png" width="300px"></a>
367 <a href="static/saxs2_10.png"><img src="static/saxs2_10.png" width="300px"></a>
368 <a href="static/saxs2_11.png"><img src="static/saxs2_11.png" width="300px"></a>
369 <a href="static/saxs2_7.png"><img src="static/saxs2_7.png" width="300px"></a>
370 <a href="static/saxs2_8.png"><img src="static/saxs2_8.png" width="300px"></a>
373 In the UNRES calculated
374 structures, the domains are at a larger angle than
375 those in the experimental NMR structure.
378 <a href="static/saxs2_13.png"><img src="static/saxs2_13.png" width="300px"></a>
381 Comparison of the input distance distributions with those calculated from the 5 models.
382 Much better agreement, in
383 particular in the long-distance part is obtained
384 for structres from the UNRES simulation.
386 <a href="static/saxs2_12.png"><img src="static/saxs2_12.png" width="300px"></a>
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