cmstultz-mollack.mit.edu

Mollack

IDP Conformational Ensemble Creation Tool. Click on "Build Ensemble" above. Upload the structural library tarball or input the primary sequence. Upload the experimental data file. Enter a job name and your email and press submit. Wait for an email with a link to the output! A downloadable version of the BW method can be found at:. Https:/ www.dropbox.com/s/y8vaqlcckwdqa48/BW Version1.1.zip. Developed by the Computational Biophysics Group at MIT.

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IDP Conformational Ensemble Creation Tool. Click on Build Ensemble above. Upload the structural library tarball or input the primary sequence. Upload the experimental data file. Enter a job name and your email and press submit. Wait for an email with a link to the output! A downloadable version of the BW method can be found at:. Https:/ www.dropbox.com/s/y8vaqlcckwdqa48/BW Version1.1.zip. Developed by the Computational Biophysics Group at MIT.

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Mollack | cmstultz-mollack.mit.edu Reviews

https://cmstultz-mollack.mit.edu

IDP Conformational Ensemble Creation Tool. Click on "Build Ensemble" above. Upload the structural library tarball or input the primary sequence. Upload the experimental data file. Enter a job name and your email and press submit. Wait for an email with a link to the output! A downloadable version of the BW method can be found at:. Https:/ www.dropbox.com/s/y8vaqlcckwdqa48/BW Version1.1.zip. Developed by the Computational Biophysics Group at MIT.

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cmstultz-mollack.mit.edu

1

Data

http://cmstultz-mollack.mit.edu/instructions.php

IDP Conformational Ensemble Creation Tool. At this point, the sources of experimental data that Mollack can use are H, Ha, N, Ca, Cb, and C chemical shifts, residual dipolar couplings, J-couplings, and the radius of gyration. Mollack calculates the ensemble values of these observables with SHIFTX for the chemical shifts, PALES for the RDC, and the Karplus equation for the J-couplings. An example is shown below for the sequence AGVD:. BMRB Chemical Shift File:.

2

Mollack

http://cmstultz-mollack.mit.edu/help.php

IDP Conformational Ensemble Creation Tool. Developed by the Computational Biophysics Group at MIT.

3

Mollack

http://cmstultz-mollack.mit.edu/index.php

IDP Conformational Ensemble Creation Tool. Click on "Build Ensemble" above. Upload the structural library tarball or input the primary sequence. Upload the experimental data file. Enter a job name and your email and press submit. Wait for an email with a link to the output! A downloadable version of the BW method can be found at:. Https:/ www.dropbox.com/s/y8vaqlcckwdqa48/BW Version1.1.zip. Developed by the Computational Biophysics Group at MIT.

4

About

http://cmstultz-mollack.mit.edu/about.php

IDP Conformational Ensemble Creation Tool. Mollack is based on the Variational Bayesian Weighting with Structure Selection algorithm developed in the Stultz Lab at MIT, which is responsible for finding weights for the structures generated by biased molecular dynamics simulations. Information about the basic Bayesian Weighting algorithm can be found here. And information about the more advanced VBWSS algorithm can be found here. Both should be cited if you use Mollack.

5

Build Ensemble

http://cmstultz-mollack.mit.edu/start.php

IDP Conformational Ensemble Creation Tool. To make an ensemble for your IDP, simply upload a tarball (.tar.gz file) with a pdb file for each structure in the library in a top level folder. Mollack can work with libraries that contain at most 2000 structures. Next, upload the experimental data that will be used to generate the weights for the ensemble. For instructions on how to format the experimental data, click here. Finally, choose a name for your job and enter your email and press submit! If you do n...

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Vls3d - Simulation

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Doctoral school for therapeutic Innovation. Computational Biology and Chemistry. Protein, DNA, RNA, Glycan modeling. Protein-protein docking, template-based docking. Hotspots, Interace residues, PPI modulators. PPI databases, network. Binding pockets and ligand-pocket datasets. Peptides, antibodies, epitopes. Visualization - commercial tools. Chemistry toolkits and utilities. Manage collections - chemical space. ADMET- physchem predictions - related tools. Off-targets, drug repurposing. An open source li...

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cmstultz-mollack.mit.edu

Mollack

IDP Conformational Ensemble Creation Tool. Click on "Build Ensemble" above. Upload the structural library tarball or input the primary sequence. Upload the experimental data file. Enter a job name and your email and press submit. Wait for an email with a link to the output! A downloadable version of the BW method can be found at:. Https:/ www.dropbox.com/s/y8vaqlcckwdqa48/BW Version1.1.zip. Developed by the Computational Biophysics Group at MIT.

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