This repository pertains to the benchmarks for testing the method to determine the optimal coarse-grained bead representation for a system given input data, a scoring function, and a sampling scheme.

It contains input data, scripts for modeling, and results including bead models and localization probability density maps. It uses IMP (Integrative Modeling Platform).

Prerequisites

Note that the results were obtained using code and scripts in the optrep module of IMP.

Folder structure

1. inputs : contains all the input data used for modeling such as PDB files, crosslink files, configuration files, and so on.
2. results : contains the optimal representations obtained, as well as final representative models.
3. scripts : scripts that are specific to the benchmark are included in this repository. For more general scripts and code, the user is referred to the optrep module.

Information

Author(s): Shruthi Viswanath

Maintainer: shruthivis

Date: October 31st, 2018

License: CC BY-SA 4.0 This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.

Publications:

• S. Viswanath and A. Sali, Optimizing model representation for integrative structure determination of macromolecular assemblies, submitted.