ISB Lab Software and Resources

Software

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

Name Description Link
Integrative modeling software
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 tutorial for optimizing replica exchange temperatures.
GitHub
Sampcon Pipeline for analyzing integrative models after MCMC sampling. Includes tests for assessing sampling exhaustiveness, clustering models, and calculating precision. GitHub
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. GitHub
Other utilities Contains scripts for calculating interface RMSD, and other utilities for modifying PDBs, adding chain names, running Modeller etc. GitHub
Database
StrIDR StrIDR is a database of IDRs, confirmed via experimental or homology-based evidence, that are resolved in experimentally determined structures. GitHub
Database



Courses and Workshops


Integrative Modeling Tutorials and Workshops

Graduate Courses at NCBS