ISB Lab Software and Resources
Software
Check out software developed by our group and other open-source freebies at ISB Lab GitHub.
IMP-related software
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.
PrISM : Package to annotate high- and low-precision regions in integrative structure models. Now used by wwPDB to validate integrative models!
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.
Sampcon : Pipeline for analysing integrative models after MCMC sampling. Includes tests for assessing sampling exhaustiveness, clustering models, and calculating precision.
Protein-protein docking-related software
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
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Statistical Inference in Biology (internal link) co-taught with Dr Shaon Chakrabarti at NCBS.
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Crash course in Python taught during the Statistical Inference course.