Supplementary Reading
A1. Claude E. Shannon 
A Mathematical Theory of Communication  (pdf)
A2. Inside the Cell
A3. The New Genetics
A4. The Chemistry of Health
A5. The Structures of Life
A6. Computing Life (Computing Life Online)
A7. RasMol and Chime
RasMol Tutorial
A8. Gerhard Wider 
Technical aspects of NMR spectroscopy with biological macromolecules and studies of hydration in solution
A9. Jenny P. Glusker 
Elementary X-Ray Diffraction for Biologists
A10. PDB Format Description
A11. B.Alberts, The Shape and Structure of Proteins
A12. E.V.Koonin, M.Y.Galperin, Principles and Methods of Sequence Analysis


Journal Articles
1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ 
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Res 1997 Sep 1;25(17):3389-402
2. Bystroff C, Thorsson V, Baker D 
HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins
J Mol Biol. 2000 Aug 4;301(1):173-90
3. Chandonia JM, Karplus M 
New methods for accurate prediction of protein secondary structure.
Proteins. 1999 May 15;35(3):293-306
4. Cuff JA, Barton GJ 
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.
Proteins. 1999 Mar 1;34(4):508-19
5. Dandekar T, Konig R 
Computational methods for the prediction of protein folds.
Biochim Biophys Acta. 1997 Nov 14;1343(1):1-15
6. Kasuya A, Thornton JM 
Three-dimensional structure analysis of PROSITE patterns.
J Mol Biol. 1999 Mar 12;286(5):1673-91.
7. Koppensteiner WA, Lackner P, Wiederstein M, Sippl MJ 
Characterization of novel proteins based on known protein structures.
J Mol Biol. 2000 Mar 3;296(4):1139-52
8. Krogh A 
An Introduction to Hidden Markov Models for Biological Sequences.
Computational Methods in Molecular Biology (Eds. S. L. Salzberg et al.) 
Elsevier,  1998. pp. 45-63.
9. Levitt M, Hirshberg M, Sharon R, Daggett V 
Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution.
Computer Physics Communications. 1995 Sep 2; 91(1-3):215-31
10. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A 
Comparative protein structure modeling of genes and genomes.
Annu Rev Biophys Biomol Struct. 2000;29:291-325.
11. Miyazawa S, Jernigan RL 
Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues.
Proteins. 1999 Jan 1;34(1):49-68.
12. Sagui C, Darden TA 
Molecular dynamics simulations of biomolecules: long-range electrostatic effects.
Annu. Rev. Biophys. Biomol. Struct. 1999, 28:155-179
13. Shindyalov IN,  Bourne PE 
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
Protein Eng 1998; 11(9):739-747.
14. Teichmann SA, Chothia C, Gerstein M 
Advances in structural genomics
Curr Opin Struct Biol 1999 Jun;9(3):390-9
15. Koehl P, Levitt M.
Sequence variations within protein families are linearly related to structural variations.
J Mol Biol. 2002; 323(3):551-62
16. Gan HH, Perlow RA, Roy S, Ko J, Wu M, Huang J, Yan S, Nicoletta A, Vafai J, Sun D, Wang L, Noah JE, Pasquali S, Schlick T.
Analysis of protein sequence/structure similarity relationships
Biophys J. 2002 Nov;83(5):2781-91
17. Bartlett GJ, Choudhary A, Raines RT, Woolfson DN.
n-->pi* interactions in proteins
Nat Chem Biol. 2010;6(8):615-620
18. Cole C, Barber JD, Barton GJ
The Jpred 3 secondary structure prediction server
Nucleic Acids Res. 36 (suppl. 2): W197-W201

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