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Expression and Purification
- SLIC cloning
- Tags
- Expression systems
- Expression screening
- Purification
- Cleavage: wanted and unwanted
- DNA and DNA-binding proteins
- Expression and Purification: Tips and Tricks
Crystals
Crystal growth and manipulation
- Modifying the protein to crystallize better
- Crystallization screens and methods
- Robots for crystallization setup
- Biophysical methods for characterizing proteins and their crystals
- Visualization of crystal growth
- Robots for crystal mounting
- Crystal growth: Tips and Tricks
Data collection
- X-ray generators and detectors (experiences)
- Synchrotron beamlines
- Cryo
- Strategies
- Data quality
- Radiation damage
- Data collection: Tips and Tricks
Crystallography
Theory
Programs
by package
(large packages first)
- CCP4
- CNS
- PHENIX
- SHELX C/D/E/L (homepage at [1])
- moleman, lsqman, ... from Uppsala Software Factory
- XDS homepage and XDSwiki
- HKL homepage
- COOT
- PyMol wiki
- O
- ARP/wARP
- SHARP homepage
- Solve/Resolve
- ...
by task
- Data reduction
- Molecular replacement (MR)
- Experimental phasing (SIR/MIR and SAD/MAD)
- Model building
- Refinement
- Model validation
- Solving a structure: Tips and Tricks
- Model building and refinement: Tricks and Tips
Bioinformatics
- Servers and programs for sequence analysis
- Structure based sequence alignment
- Servers and programs for protein structure analysis
- Programs for nucleic acid structure analysis
- Servers for ligand topologies/parameters
- Prediction of structure from sequence: servers and programs
- Programs for visualization (see also Model building)
- Links to Bioinformatics websites
Hardware: computing and displaying
- Computer hardware
- Operating systems and Linux distributions
- Programming and programming languages
- Graphics cards and 3D
FAQ and troubleshooting
- protein is not expressed or cannot be purified
- crystals don't grow
- phases too bad
- model does not refine