TA: Sid Chaudhury
Computer lab session: M 3:00-4:00, Jenkins 122
Email: sidc [at] jhu.edu

Recommended software: PyMol

• Syllabus
• Mid-semester Survey (please complete by March 31)
• Jenkins Lab Registration

• Homework #1
• Homework #2
• Homework #3
• Homework #4
• Homework #5
• Homework #6
• Homework #7
• Project and Peer Evaluation Form

• Workshop #1: PyMol
• Workshop #2: PyRosetta for Protein Structure
• Workshop #3: PyRosetta for Protein Scoring
• Workshop #4: PyRosetta for Protein Folding
• Workshop #5: PyRosetta for Refinement
• Workshop #6: PyRosetta for Side-Chain Packing and Design
• Workshop #7: PyRosetta for Docking
• Workshop #8: PyRosetta for Loops (includes Fold Tree)
• PyRosetta Reference Sheet (updated April 9)

• 2008 Exam 1 from ChemBE 460/660
• Learning Objectives updated for the Final Exam

Readings and References

• Week 1: Protein structure
  1. Brandon & Tooze Ch. 1 (1999)
  2. Brandon & Tooze Ch. 2 (1999)
  3. Richardson, "Anatomy & Taxonomy of Protein Structure" (1981; updated 2000-2007, for ChemBE 614 students)
  4. Amino acid crib sheet
  5. PyMol Reference Sheet
  6. An example PyMol script that colors an antibody for easy manipulation: antibody_selections.pml
     It works nicely on 1bql.pdb
• Week 2: Protein geometry
  1. Engh & Huber (1991), Bond lengths and angles reference
  2. Parsons et al. (2005), Torsion to Cartesian formulas reference (beware of typos!)
  3. Python documentation (try the tutorial and language reference)
  4. Rosetta documentation
• Week 3: Energy functions
  1. Neria, Fischer & Karplus (1996), CHARMm19 parameters for VdW and electrostatics (reference)
  2. Kortemme et al. (2003), Hydrogen bonding potential with Supplemental Material (reference)
  3. Eisenberg & McLachlan (1986), Atomic solvation parameters for SASA potential (reference)
  4. Lazaridis & Karplus (1999), Pairwise Gaussian solvation model (reference)
• Week 4: De novo folding
  1. Simons et al. (1997), "Assembly of Protein Structures from Fragments"
  2. Simons et al. (1999), "Improved Recogntion of Protein Structures"
• Week 5: Refinement
  1. Bradley et al. (2005), "Toward High-Resolution de Novo Structure Prediction for Small Proteins"
  2. Supplemental Material
• Week 6: Side chain packing and rotamer libraries
  1. Lovell et al. (2000), "The Penultimate Rotamer Library"
  2. Desmet et al. (1992), "The Dead-End Elimination Theorem and Its Use in Side-chain Positioning"
  3. Dunbrack & Cohen (1997), "Bayesian Statistical Analysis of Protein Side-chain Rotamer Preferences"
• Weeks 7-8: Design
  1. Reading Discussion 1: Design for Structure
  2. Reading Discussion 2: Design for Function
• Week 9: Docking
  1. Gray et al. (2003) RosettaDock Protein-Protein Docking
  2. Chaudhury & Gray (2008) Conformer Selection and Induced Fit Docking
• Week 10: Loop modeling
  1. Canutescu & Dunbrack (2003) Cyclic coordinate descent
  2. Wang, Bradley & Baker (2007) Fold trees
• Week 11: Homology modeling
  1. Bordoli, Schwede et al. (2009) SWISS-MODEL
• Week 12: Enzyme Design
  1. Zanghellini et al. (2006) Enzyme design benchmark
  2. Rothlisberger et al. (2008) Kemp elimination