CrocoBLAST:UserManual

Below you can find the CrocoBLAST user manual, which contains all the information you need in order to make efficient use of CrocoBLAST. Note that you need not install CrocoBLAST, as it is sufficient to download the files from the webpage and unzip them. You may run CrocoBLAST from the graphical interface or directly from the command line. Using the graphical interface currently requires Java - but don't worry, you probably have it already. If you get in trouble, see the Technical details page.

Happy sequence munching! Nom nom!

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Terminology

1. Structural elements
   1. Molecule
   2. Atom
   3. Residue
2. Charges
   1. Atomic charge
   2. Residue charge
   3. Molecular charge
3. Work flow
   1. Atom type
   2. Atom type scheme
   3. EEM parameters
   4. EEM parameter sets
   5. Computation method
   6. Job
   7. Charge set

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Job submission

1. Upload molecules
2. Setup computation
   1. Set total charge
   2. Pick EEM parameters
   3. Pick computation method
3. Start computation

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Interpretation of results

1. Synopsis page
2. Specifics page
   1. Summary
   2. Raw Data
   3. Analyze
   4. Compare
   5. 3D Model

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Case studies

1. Paracetamol
2. Apoptosis
3. Proteasome

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Technical details

1. Requirements
2. Limitations and troubleshooting

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Theoretical background

1. EEM
2. EEM Cutoff
3. EEM Cutoff Cover

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