ISB Lab Software and Resources



Software

Check out software developed by our group and other open-source freebies at ISB Lab GitHub.

Many of the packages we develop are integrated with the Integrative modeling Platform IMP, which we use to model protein assemblies.

NestOR : Nested sampling-based optimization of representation for integrative structural modeling.
GitHub

PrISM : Package to annotate high- and low-precision regions in integrative structure models. Now used by wwPDB to validate integrative models!
GitHub

StOP : Stochastic Optimization of Parameters (StOP) automates the tuning of MCMC parameters for stochastic sampling in IMP. - Check this tutorial for optimizing Monte Carlo move sizes/restraint weights.
- And this one for optimizing replica exchange temperatures.
GitHub

Sampcon : Pipeline for analysing integrative models after MCMC sampling. Includes tests for assessing sampling exhaustiveness, clustering models, and calculating precision.
GitHub

Scoring functions: PISA (atomic), PIE (residue), and C3 (combination) scoring functions for ranking models of protein-protein complexes produced by docking programs.

Other utilities: Contains scripts for calculating interface RMSD, and other utilities for modifying PDBs, adding chain names, running Modeller etc.

Courses and workshops



Integrative modeling tutorials and workshops

Graduate courses at NCBS