True Advantage - Protein Crystallography


Bioinformatic Tools

  • NCBI: Biomedical and genomic information
  • NCBI BLASTp: Protein sequence alignment
  • PSI-PRED: Secondary structure prediction
  • ClustalOmega: Sequence alignment
  • PFAM Database: Collection of protein families
  • FATCAT: Flexible structure alignment
  • POSAFlexible multiple structure alignment
  • XtalPred: Prediction of protein crystallizability
  • FFAS: Fold and function assignment
  • SERp: Surface entropy reduction
  • CheckMyMetal: Metal binding site validation
  • Multiple Sequence alignment WebLogo [8] - frequency of amino acid positioning
  • MODELLER [12] - MODELLER license key is MODELIRANJE
  • Phyre [13] - structure prediction
  • Transmembrane prediction [15]
  • Evaluating homologs - maintain conserved sequences, look for pI differences, try full-length constructs before truncations unless hydrophobic/predicted TM domain, shorter length and divergent primary sequences can be good
  • Identifying rare codons [16]
  • Helical wheel generator [17] [18]

 

Literature Search Tools

  • NCBI PubMed: Collection of Biomedical Literature
  • PaperBLAST: Locate papers about a specific protein and homologs

 

Structural Biology Tools

  • Protein Data Bank: Collection of protein structural models
  • ModWeb: Protein structure modeling
  • Phyre2: Protein homology modeling
  • ProtMod: Protein structure modeling
  • I-TASSER: Protein structure and function predictions
  • QwikMD: Molecular dynamics simulation tool
  • DALI: Protein structure comparison
  • PyMol: Molecular visualization system (recommended for beginners)
  • VMD: Molecular visualization program
  • Chimera: Interactive visualization and analysis tool

Structural Biology Guides

Practical Protein Crystallography

 

 

Protein Crystallography Theory

 

Review Biochemistry Basics.

Crystallography Basics: From Proteins to Crystals, Crystals and Entropy, The humble Braggs

Recommended Reading:

E. Lattman & P. Loll. Protein Crystallography. A Concise Guide.  Johns Hopkins University Press, Baltimore.  2008

Lectures:

Additional Resources:

Nucleation

Crystal Growth

Anti-gravity promotes ordered crystal growth by eliminating convection currents