MISHAP
Monday, 15th April 2013

MISHAP

MISHAP shall not be made available for general release until the associated manuscript is completed.

Latest build: 22nd August 2013 (v13.08-BETA)

The MMM Interfacing of Spin labels to HADDOCK Program is a collection of MatLab scripts, graphical user interfaces and custom definition files that allows for the taking of a protein model with attached EPR spin labels of MTSL or IA-PROXYL from the Multiscale Modeling of Macromolecular systems program (MMM) and combine it with distance distribution information either from MMM in silico calculations or from PELDOR / DEER (pulsed electron-electron double resonance) experiments analysed with DeerAnalysis as docking restraints within the protein docking program HADDOCK.

The sub-programs

MISHAP is the umbrella term for a program of many parts, each performing it’s own task to achieve the end goal.

The MISHAP installer

The installer performs 2 tasks. The first is that it modifies MMM so that MISHAP can be called from MMM using the Predict > Quarternary > HADDOCK menu. Second if HADDOCK is to be run locally then it needs to be updated with definitions for the MTSL and IA-PROXYL attached CYS residues.

The PDB creator

The PDB creator pulls a model from MMM and saves a protein chain as a HADDOCK compatible PDB, as HADDOCK requires a specifically stripped PDB format which MMM could not generate.

The main MISHAP window

The main MISHAP window is responsible for the loading of distance distribution data from MMM or DeerAnalysis. If either program is open then it will source the data automatically, otherwise it will prompt the user to open a saved distance distribution. It will then automatically guess the best parameters – to which the user should check. When the user is happy an HADDOCK unambiguous distance restraints file is generate.

The MISHAP generated PDBs combined with MISHAP restraints file can then be passed to HADDOCK for docking.

Acknowledgments

This program would not be made possible without the hard work of:

The ETH Zurich EPR team namely Gunnar Jeschke and Yevhen Polyhach.

The Utrecht University HADDOCK team namely Alexandre Bonvin and João Rodrigues

The Worldwide e-Infrastructure for NMR and Structural Biology (WeNMR)

About Morgan Bye

Scientist, programmer and all around techie

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