The lab uses a range of computational approaches, many of which we are actively developing. A subset of these tools are listed below. The development of novel tools and approaches is central to our ability to ask new types of questions.
CAMPARI is an all-atom simulation engine that performs both Monte Carlo and Molecular Dynamics simulations. CAMPARI is optimized to work with the ABSINTH implicit solvent model, and was developed by Andreas Vitalis in the Pappu lab. The Pappu lab, Andreas Vitalis, and Holehouse lab continue to develop aspects of CAMPARI, ABSINTH, and associated simulation analysis tools in a collaborative manner.
PIMMS (Polymer Interactions in Multicomponent MixtureS) is a high-performance coarse-grained lattice-based simulation engine developed explicitly for studying phase transitions of complex heteropolymers, such as intrinsically disordered proteins. PIMMS was developed by Alex while in the Pappu Lab, and is a MOLSSI sponsored project.
CIDER & localCIDER
CIDER is a webserver for the analysis of protein sequences. It provides a simple interface to interact with protein sequences. CIDER is a web interface to localCIDER, an interaction Python API for analyzing sequence features of intrinsically disordered proteins. CIDER and localCIDER were developed by Alex while in the Pappu lab.
ShanEnt is a high-performance Python tool-kit for whole-proteome analysis to identify statistical signatures in proteomes. ShanEnt is currently being developed by junior research scientist Garrett Ginell, working with Alex.
CTraj is an integrative analysis suite for analyzing all-atom simulation trajectories of intrinsically disordered proteins. CTraj was developed explicitly with CAMPARI Monte Carlo simulations in mind, but is directly applicable to simulations performed with almost any simulations engine and trajectory type. CTraj was developed by Alex while in the Pappu lab, and is a MOLSSI sponsored project.
SolutionSpaceScanner is a Python toolkit that includes a command-line tool for re-wiring the solvation behaviour of polypeptides by creating customizable parameter-files for the ABSINTH implicit solvent model. SolutionSpaceScanner was developed with the Sukenik lab at UC Merced and is a MOLSSI sponsored project.
DOWNLOAD (release candidate June 30th 2019)