Complete automation in CCP4 What do we need and how to achieve it?

Starting point Given data and experimental setup (protein name or sequence, crystallisation condition(s), probable ligands) to solve the structure, complete refinement with complete model building, fit ligand(s), validate (against experiment as well as prior knowledge), do early analysis or calculations to help early analysis. All calculations and decisions should be made automatically I estimate success rate using current technology roughly around 80% (may be more).

Overall view Interpretation DATA Optimisation feedback data MR/heavy atom/ab in Interpretation DATA Optimisation feedback data Critical eval Validation Completion Early analysis

Aim: Automation of X-ray Analysis (Equivalent to Microscope) Data Data base of chemical, structural knowledge Molecular replacement Experimental phasing Refine/Build/Rebuild Refine/Complete ! Final structure

Knowledgebase: Discuss Structural knowledge domains, multimers, rotamers, links between similar structures, fragments and their properties. Crystals - cells, intensities, solvent contents, resolutions … Chemical knowledge Monomers and their valence bond chemistry Possible modifications Smaller structural units Protocols and structure solution techniques How to organise them? How to use them?

Components DATA – Experimental data, sequence/protein name, crystallisation condition(s), ligand(s) Interpretation – Using DB and accumulated knowledge build the model Optimisation - Refine the model against data and prior knowledge Criticism – Is model consistent with the data and prior knowledge. Some of the prior knowledge may have not been used in optimisation Feedback data – Electron density map, information about misfitted parts, new prior information taken from the DB Completion – Tidying up waters, multiple conformation, hydrogen bonding network. Are there heavier atoms. Etc Validation – Is model consistent with data and prior knowledge. More sophisticated analysis Early analysis – Is there similar structures, family of proteins, similarity of ligand binding etc.

Information flow What is needed by the next stage? In the absence of previous step how to generate necessary information? CCP4i works partially deals with this.

Feedback data: discuss!

Components: Cont Completion – that is at the moment not very well worked out part of the whole system. It requires careful analysis of waters, hydrogen bonding network, multiple conformation. Ligand fitting need to be done here if it has not already been done. For ligands we can use several techniques: For large ligands we can use divide and conqure. I.e. divide ligand into smaller building blocks and try to fit them first and then try to make sense of things. For small ligands we need to generate all possible conformations and try to fit them one after another and score according to experimental data as well as prior knowledge.

Components: Cont Each component should be independent. It means that they can be replaced at any time with another “better” component. User should be able to enter at any point. For example user can start from interpretation. The system will have to be able to work with minimal information. Data Base of knowledge is very important component. It needs to be worked on very carefully.