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Protein structures, databases and servers Unit 24

Protein structures, databases and servers Unit 24. BIOL221T : Advanced Bioinformatics for Biotechnology. Irene Gabashvili, PhD. Protein structure. Primary structure (Amino acid sequence) ↓ Secondary structure （ α -helix, β -sheet） ↓

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Protein structures, databases and servers Unit 24

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  1. Protein structures, databases and serversUnit 24 BIOL221T: Advanced Bioinformatics for Biotechnology Irene Gabashvili, PhD

  2. Protein structure Primary structure (Amino acid sequence) ↓ Secondary structure（α-helix, β-sheet） ↓ Tertiary structure （Three-dimensional structure formed by assembly of secondary structures） ↓ Quaternary structure （Structure formed by more than one polypeptide chain）

  3. The DSSP code "Dictionary of Protein Secondary Structure" G = 3-turn helix (310 helix). Min length 3 residues. H = 4-turn helix (alpha helix). Min length 4 residues. I = 5-turn helix (pi helix). Min length 5 residues. T = hydrogen bonded turn (3, 4 or 5 turn) E = beta sheet in parallel and/or anti-parallel sheet conformation (extended strand). Min length 2 residues. B = residue in isolated beta-bridge (single pair beta-sheet hydrogen bond formation) S = bend (the only non-hydrogen-bond based assignment)

  4. Databases PDB: www.rcsb.org/ MSD: http://www.ebi.ac.uk/msd/ MMDB: http://www.ncbi.nlm.nih.gov/Structure/MMDB PDBSum: www.biochem.ucl.ak.uk TargetDB: targetdb.pdb.org/

  5. Prediction Homology Modeling Threading Ab initio structure prediction Similarities & Differences

  6. Validation DSSP PROCHEK VADAR Verify3D

  7. Visualization Cn3D UCSF Chimera (Midas) Rasmol ProteinExplorer http://www.umass.edu/microbio/rasmol/

  8. Cn3D Cn3D is a visualization tool for biomolecular structures retrieved by NCBI's Entrez. Cn3D simultaneously displays structure, sequence, and alignment, and has annotation and alignment editing features (Windows, Macintosh, and Unix).

  9. Cn3D

  10. Style  Edit Global Style

  11. CHIMERA MOLECULAR MODELING SYSTEM http://www.cgl.ucsf.edu/chimera/ Chimera is an interactive molecular graphics program. More advanced than Cn3D or Rasmol, Python scripts

  12. Chimera demo Tools > Structural analysis > distances

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