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Integrative structures of the Nef-CD4-AP2 complex

Integrative structure of the Nef-CD4(CD)-AP2(Δμ2-CTD) complex PubMed logo PDB-Dev

warningThese files work only with a nightly build of IMP on or after 2020-08-14, not the stable release. The files are also available at GitHub.
Additional software needed to use these files: IMP numpy MODELLER install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp numpy modeller

UCSF logo To set up the environment on the UCSF Wynton cluster to run this system, run:

module load Sali
module load imp python3/numpy modeller
Tags chemical crosslinks MODELLER PMI X-ray

Integrative structure of the Nef-CD4(CD)-AP2(Δμ2-CTD) complex

DOI

These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the solution structure of the Nef-CD4-AP2 complex using 90 DSSO chemical cross-links and the X-ray structure of the crystal structure, a comparative model of the β2 subunit 24-89 region built based on the AP2 structure.

First, MODELLER is used to generate comparative model of the β2 subunit 24-89 region. Then, IMP is used to model these components using crystal structure and the DSSO crosslinks to obtain the solution structure of the Nef-CD4(CD)-AP2(Δμ2-CTD) complex.

The modeling protocol will work with a default build of IMP, but for most effective sampling, IMP should be built with MPI so that replica exchange can be used.

List of files and directories:

Running the MODELLER scripts:

Running the IMP/PMI scripts for the Nef-CD4(CD)-AP2(Δμ2-CTD) complex:

Next, analyze resulting models (this script can also be used to combine results from multiple independent runs):

Information

Author(s): Ignacia Echeverria

Date: May 5th, 2020

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Last known good IMP version: build info build info

Testable: Yes.

Parallelizeable: Yes

Publications: