CCP4 Molecular Replacement Model Generation

Create a CCP4i task for generating Molecular Replacement models.

- Selecting suitable PDB entries, based on e.g. sequence

- Producing the best search model from these PDB entries.(altered sequence, multimers, conformational variants)

Technical aspects:

- Database searching – local vs remote?

- Relationship to target selection and construct design.

Charlie Bond, Airlie McCoy, Martyn Winn, Ronan Keegan, Alexei Vagin, Garib Murshudov, Geoff Barton, Ian Overton, (Charles Ballard, Kim Henrick) Level of

discussion

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Initial goals

- Get CHAINSAW developed, released and into CCP4i (Norman/Fei)

- Get Normal Mode Analysis model generation into the suite (Airlie, Charles)

- Develop database searching - which tools are suitable and available (Martyn, Ronan, Geoff, Kim)

- Investigate how information from construct design steps may be used for model design (Charlie, Geoff, Ian)

What in now in the suite

(1) Selecting suitable PDB entries, based on e.g. sequenceMrBUMP

(2) Producing the best search model from these PDB entries.Altered sequence: CHAINSAW GUI (and MrBUMP), MOLREPMultimers: MrBUMPConformation: NMA (in PHASER GUI)

(3) Standalone vs NetworkLocal databases, local search software:- MOLREP? MrBUMP (local fasta)Remote databases, local search software- MrBUMP (fasta client:EBI server)Remote databases, remote search software- MrBUMP (SOAP interface to EBI webservices)

(4) Relationship to construct design etcPIMS/SSPF: TarO (next slide)

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TarO: SSPF Target Optimisation Pipeline (Ian Overton, Geoff Barton @ Dundee)

PIMS-friendly

Input sequence -> builds alignments (COG, UNIREF)-> predicts 'crystallisability' -> checks ASTRAL for similar structures -> globularity predictions etc. -> (in future) domain identification.

Performed for all SSPF targets to select most appropriate ortholog/truncation to take forward for cloning ... crystallography.

Takes an hour or two to run.

In principle, provides far superior alignments in borderline cases to simple clustalw alignment.

Ian is considering ways of providing output from TarO which is suitable for model generation, such as CHAINSAW-friendly sections of alignments and links to structure databases.

CCP4's Model Generation Arsenal

Production of a good model generation task needs to be part of a complete reorganisationof the molecular replacement tools in the GUI

The Next Steps...

Get CHAINSAW and NMA (and multimers?) into a single GUI.

Use MrBUMP as a basis? Allow different entry points and exit points.Entry:Single sequencePredetermined seed alignmentPredetermined alignment to PDBExit:Option to not continue into MR.

This should be in the context of completely restructuring the CCP4i MR menu.

Personal Perspective

GUI – Who are the users?

We have to be careful about providing appropriate tools

Traditional crystallographerSomeone gave me a protein to crystallise. I've now collected data. I'll ask them for the sequence and see if we can find a molecular replacement model

Speed freakCan the robot solve targets xyz00001-99999 by molecular replacement? We already built alignments and analysed domains before we even cloned them

Biochemist/molecular biologist/structural biologist/biological chemist...I love this protein, I know everything about it, and have excellent hand-crafted alignments and masses of anecdotal non-machine-readable data.