The original UNRES-SERVER tutorial from 2018

In order to submit a job you need to provide its name:

The following three types of simulations which can be run with the UNRES server are described in this tutorial: local minimization, molecular dynamics and replica exchange molecular dynamics. The dock and and aggregation type of simulation are show in seperate tutorials.

Use the "Save & submit" button to start calculations.

Use the "Refresh" button to check the status of a simulation:

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After the server job has been submitted the "waiting in the queue to start" message will be displayed in the status field, which will subsequently change to "running", "postprocessing", and "done". While the job has the "running" status, the percentage of job accomplishment is displayed. It should be noted that the "100%" accomplishment refers to the production phase of a job, after which the postprocessing phase is triggered which also takes some time (up to several minutes when making a movie from an MD trajectory is requested) and whose progress is not monitored. The page is autorefreshed every 30 sec.

Any single job can by accessed later (for at least 14 days) using the address of the web page displayed after job submission: e.g. http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
Registered users can save all their jobs and access them later after logging in. Note that the results will be available for a limited period of time, depending on the storage space availability (at least 30 days).

You can use "Load example data" button before submitting calculations to try examples listed below:

Local minimization of protein A (PDB code:1BDD) structure

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In this example only the PDB code of the selected protein (1BDD) is input.

After energy minimization is accomplished, the UNRES model of the protein, its total UNRES energy and superposition on starting structure are displayed. The interactive NGL Viewer is employed, which enables the users to manipulate the structure.



All files generated during calculations can be viewed/download by clicking on the "Directory" link.

Molecular dynamics of IGG-binding domain from streptococcal protein G (PDB code:1IGD) starting from the experimental structure

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After the MD simulation is accomplished temperature histogram, plots of UNRES energy, RMSD from the experimental structure, fraction of native contacts, and radius of gyration vs. time, a movie of the trajectory, and CA-atom fluctuations are displayed.



Evolution of RMSD, fraction of native contacts and comparison of CA fluctuations to Bfactor is presented only when the reference structure is provided, as in this example.

Replica exchange molecular dynamics of the Trp-Cage miniprotein (PDB code:1L2Y) starting from the extended chain

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After a (M)REMD run is accomplished, a table showing replica-exchange statistics (a), plots of histograms of UNRES energy for each temperature (b), a plot of energy vs. temperature (c), a temperature-colored scatter plot of energy vs. RMSD (d), and the temperature-colored cumulative plot of rmsd vs. step number for all replicas (e), and a cumulative plot of walk of the replicas in temperature space (f) are displayed. The colors corresponding to replica temperatures are shown in panel (c), while different replicas are colored from black to yellow in panel (f).

(a) (b) (c) (d) (e) (f)

The weighted histogram analysis method (WHAM) is applied to compute the probabilities of the obtained conformations to occur at particular temperatures and, consequently, the plots of heat capacity (g) and ensemble-averaged RMSD (h) as a functions of temperature; these are shown in the respective graphs.

(g) (h)

Note! Panels are labeled in this tutorial only and labels are not displayed in the outputs from real server jobs.

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 Download button.

Minimization of the P8MTCP1 disulfide-bonded helical hairpin miniprotein (PDB code: 1EI0).

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In this example the PDB code of the selected protein (1EI0) and the OPT-WTFSA-2 force field are selected:

After the minimization is accomplished, the UNRES model of 1EI0 protein with two disulfide bonds as read from the respective PDB file, its total UNRES energy and superposition on the starting structure are displayed:



Canonical MD simulations of the Trp-Cage miniprotein (PDB code:1L2Y) starting from the extended chain.

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In this example the PDB code of the selected protein (1L2Y) and option to write trajectory as a PDB file are selected, saving trajectory as a PDB file allows its 3D visualisation by NGL Viewer in addition to the movie which is always generated from the MD trajectory


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After the MD simulation is accomplished temperature histogram, plots of UNRES energy, RMSD from the experimental structure, fraction of native contacts, and radius of gyration vs. time, and a movie of the trajectory are displayed.



The CA fluctuations are not analyzed for start from the extended structure because of large scale conformational changes during folding.

MREMD simulations of 5G3Q:B (CASP12 target T0882)

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This simulation starts from the 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. The Berendsen thermostat was employed and the resulting conformational ensemble was clustered at the temperature of 290K. This is a full-blown structure-prediction run, but shorter compared to the UNRES runs during the CASP exercises.


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The output items are the same as those discussed with the Basic mode Example 3.



The final models are shown using NGL Viewer. PDB files can be downloaded by clicking on the Download button. The RMSD of model 1 from the experimental structure is 3.6 A and the GDT_TS is 58.8 %



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Distance distribution restrained (simulated SAXS data) replica exchange molecular dynamics of Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
(Use Load SAXS 1 example button in advanced mode)

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The output items are the same as those displayed with the Basic mode example 3. Additionaly the input reference distance distribution and distance distributions for 5 final models are plotted.



Finally models.



Comparison of the input distance distributions with those calculated from the 5 models.



Distance distribution restrained (real SAXS data) replica exchange molecular dynamics of the central portion of Factor H (PDB code:2KMS).
(Use Load SAXS 2 example button in advanced mode)

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REMD simulation starts from the experimental NMR structure (the first model is taken as the input structure). Secondary structure restraints are used. Only a short (50 energy evaluations) initial minimization is requested. The distance distribution has been downloaded from the SASBDB database (the SASDA25 entry).
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The input items are the same as those in the Advanced mode Example 2.



Final models. In the UNRES calculated structures, the domains are at a larger angle than those in the experimental NMR structure.



Comparison of the input distance distributions with those calculated from the 5 models. Much better agreement, in particular in the long-distance part is obtained for structres from the UNRES simulation.