by Peter Nollert
November 16, 2010 02:54
This is my list of indispensable online tools that I would encourage every protein crystallizer to use during different phases of the protein crystallization endeavour:
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Name
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When and how to use this online tool for your protein crystallization project
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Mentioned in this 'Protein Crystallization Hits' blog post
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PDB (RCSB) and PDBsum
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Find out if the structure of the protein you're trying to determine has been determined previously: the Information Portal to Biological macromolecular Structures (see REMARK 280 in PDB headers). Some annotated crystallization conditions of published protein structures.
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PDBsum rocks for crystallization protocols
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XtalPred Server
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Design of expression constructs. Predict the crystallizability of your designed amino acid sequence. Focus on the best expression constructs.
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Will my Protein Crystallize?
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BMCD
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Before setting up the crystallization trial: find detailed crystallization parameters of the actual or related proteins using the Biological Macromolecule Crystallization Database (currently down?)
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Temperature Scouting to Increase Protein Crystallization Success
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BRENDA
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If you're working with an enzyme, start here for construct design, purification and crystallization information: Braunschweig Enzyme Database stores information on expression, purification and crystallization of enzymes.
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Enzyme Crystallization Head-Start with BRENDA
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E-Wizard
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Design a new crystallization screen from scratch based on starting conditions from the BMCD or BRENDA. Quick online design of a new crystallization screen and download of conditions in a file
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Rational Protein Crystallizationn Optimization Schema
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Salt Crystal Predictor
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Salt or Protein crystal? Check here to to predict if that condition is prone to generate salt crystals.
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Cryoprotectant Database for Protein Crystals
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You've got crystals! Find methods and protocols for proper protein crystal freezing (cooling) and cryoprotectants that have worked previously with particular precipitation conditions.
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E-Wizard
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Crystals don't diffract well? Optimize your crystallization hit by systematically adjusting the parameters (salt, pH, polymer, additive, precipitation reagent). Quick online design of a new crystallization screen and download of conditions in a file
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Rational Protein Crystallizationn Optimization Schema
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While there's some overlap with Sean's list over at P212121.com, he has a lot of additional tools listed that relate to up- and downstream crystallization processes. Sean's blog is definitely worth a visit!
All the best,
Peter
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Tags: Online Tools