Title: In silico modeling of arch-3: Medeller and RosettaCM model building.

Type Dataset Dmitrii M. Nikolaev (2016): In silico modeling of arch-3: Medeller and RosettaCM model building.. Zenodo. Dataset. https://zenodo.org/record/226029

Author: Dmitrii M. Nikolaev ;

Links

• Item record in Zenodo
• Digital object URL

Summary

Here are all the files nessesary for prediction of archaerhodopsin-3 structure using Medeller or RosettaCM algorithms. 

For modeling using  Medeller  please read README_MEDELLER file for all the information. For RosettaCM:

Please, before using these scripts adjust them for you cluster. You will need the recent version of Rosetta package installed.

Let's take for example stucture P96787 (arch-3) as a query, 1UAZ_full.pdb as a template.

Also, you'll need grishex.script, thread.script, hybridize.script, relaxate.script, stage1_membrane.wts, stage2_membrane.wts, stage3_rlx_membrane.wts, uuu.grishin, rosetta_cm.options, rosetta_cm.xml, relax.options, cluster.options that are located in the  "GENERAL" folder here. Let's assume they are located in the workfolder.

Create an alignment file. For pairwise alignement use AlignMe/MP-T. Copy the alignment information in the file P96787_1UAZ.aln in the workfolder.

Put in the workfolder attached P96787_3.frags P96787_9.frags attached here -- fragment files for Rosetta. Put in the workfolder attached P96787.octopus.

mv 1UAZ_full.pdb 1UAZ.pdb

Open the grish.script and check: "target" and "templateA" which describe each line of the alignment file change on the names of the lines in your alignment file! For example for AlignMe it will be P96787 1UAZ. ./grishex.script P96787 1UAZ

./thread.script P96787 1UAZ

Run the hybridize script: ./hybridize.script P96787 1UAZ 500 It will take several days.

It will create file hybridized_P96787.out -- a binary silent file of 500 structures with the rebuilt loops and inserted fragments, if there were gaps. It will take several days also.

Run the ./relax.script P96787 50   It will create file relaxed_P96787.out -- a binary silent file of 25000 structures -- 50 for each hybridized.

Time to evaluate the results.

Clustering.

Run ./do.script P96787 open LISTIK delete the _0001 in the end of each line. Run ./resulting1.script

In the folder PDBSS open cluster_summary.txt. The first structure in the list is the best one. It is located in the folder PDBSS.

More information

• DOI: 10.5281/zenodo.226029

Dates

• Publication date: 2016
• Issued: December 31, 2016

Rights

• https://creativecommons.org/licenses/by/4.0/legalcode Creative Commons Attribution 4.0 International
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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