Computer Science 590.02
Topics in Computational Structural Biology

1. Introduction to Protein Structure, Branden, C. and Tooze, J. (1991) Garland Publishing, New York
   

2. Biochemistry, Stryer, L., (1995) 4th edition, W.H. Freeman & Co., New York
   

3. SICP. Abelson and Sussman's textbook "Structure and Interpretation of Computer Programs."
   We will call this book SICP.
   You can buy this book, but it is freely available online:
   URL:
   • HTML online.
     
   • SICP GitHub Ebook Edition (very cool)
     Do you want to be a computational biologist or computational chemist? Many of us use GitHub.

4. Introduction to Algorithms is a book by Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest, and Clifford Stein. The first edition of the book was widely used as the textbook for algorithms courses at many universities[1] and is commonly cited as a reference for algorithms in published papers, with over 8900 citations documented on CiteSeerX.[2] The book sold half a million copies during its first 20 years.[3] Its fame has led to the common use of the abbreviation "CLRS" (Cormen, Leiserson, Rivest, Stein).

Some other papers you may read

1. Rick Lathrop Lab
2. Other papers we may read include:
   Date: TBA
   
   • Presenting: TBA
     Protein Similarity
     Reading:
     • Protein Similarity from Knot Theory and Geometric Convolution
       CMU-CS-03-181 by Michael A. Erdmann
       J Comput Biol. 2005 Jul-Aug;12(6):609-37.

Some Useful References for the Course

Protein Science

• Introduction to Protein Structure, Branden, C. and Tooze, J. (1991) Garland Publishing, New York
• Proteins, Creighton, T.E. (1993) 2nd edition, W.H. Freeman & Co., New York
• Principles of Protein Structure, Schulz, G.E. and Schirmer, R.H. (1979) Springer-Verlag, New York
• Protein Structure - New Approaches to Disease and Therapy, Perutz, M. (1992) W.H. Freeman & Co., New York
• Enzyme Structure and Mechanism, Fersht, A.R. (1976) 2nd ed., pub. W.H.Freeman & Co., New York

Biochemistry

• Biochemistry, Stryer, L., (1995) 4th edition, W.H. Freeman & Co., New York
• Biochemistry, Voet, D. and Voet, J.G. (1995) 2nd edition, John Wiley & Sons, New York
• Principles of Biochemistry, Zubay, G.L., Parson, W.W. and Vance, D.E. (1995) Wm. C. Brown, Dubuque, Iowa

Cell Biology

• Molecular Cell Biology, Darnell, J., Lodish, H. and Baltimore, D. (1995) 3rd edition, W.H. Freeman & Co., New York
• Molecular Biology of The Cell, Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K. and Watson, J.D. (1994) 3rd edition, Garland Publishing, New York