UCR Biomolecular Modeling Workshop
Hands-on tutorial on structural modeling

Dimitrios Morikis, Ph.D.
Department of Chemical & Environmental Engineering
University of California at Riverside
Riverside, CA 92521
909-787-2696
dmorikis@engr.ucr.edu
http://www.engr.ucr.edu/~dmorikis

Table of Contents

  1. Preparation Familiarization with basic features of DeepView/SPDBV
  2. Exercise 1: Analysis of structure quality and basic structural characteristics
  3. Exercise 2: Structural alignments, work with 2 or more proteins
  4. Exercise 3: Analysis of the catalytic site of a an enzyme and energy minimization
  5. Exercise 4: Analysis of dimerization interfaces and construction of theoretical point mutations
  6. Exercise 5: Loop building
  7. Exercise 6: Electrostatic potentials and their role in protein-protein interactions

References

  1. Protein Data Bank (or Research Collaboratory for Structural Bioinformatics)
  2. Expasy Molecular Biology Server (Expasy: EXpert Protein Analysis System)
  3. SWISS-PROT Protein Knowledgebase
  4. Swiss Model
  5. Deep View-Swiss PDB Viewer

Additional files

  1. 1MBN.pdb
  2. 1A6G.pdb
  3. 1GDI.pdb
  4. 1BIN.pdb
  5. 1CDE.pdb
  6. 1GAR.pdb
  7. 2GAR.pdb
  8. 3GAR.pdb
  9. 1GHQ.pdb
  10. p02238.txt
  11. myfile.txt
  12. myfile.fst