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National University of Singapore, Science Faculty, Computational Sci Dept
 
   
   

CZ5225 Modeling and Simulation in Biology (Elective, 4MC)


Synopsis
Prerequisite: CZ3252
Proteins: sequence => structure =>function. Protein structural organizations and families. Basic modeling and simulation techniques. Protein structural modeling: homology modeling, threading, ab initio methods. Cell as a complex machine: Genetic and protein circuits (pathways). Development
of a mathematical model of pathways. Computer simulation of pathways.

Instructor
Dr. Chen Yu Zong
Department of Computational Science
National University of Singapore
Office: Blk S17 Room 07-24
Tel: 6874-6877. Fax: 6774-6756
E-mail: yzchen@cz3.nus.edu.sg
Web: http://www.cz3.nus.edu.sg/~yzchen
(Lots of info about biocomputing)

Lectures:

Archived Lectures and Projects in 2007/2009:

 

Archived Lectures and Projects in 2005/2006:

 

Archived Lectures and Projects in 2004/2005:

References:

Protein families:

  • A genomic perspective on protein families. Science 278, 631-637 (1997)
  • Unification of protein families. Curr. Opin. Struct. Biol. 8, 372-379 (1998)
  • Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307, 1113-1143.
  • Transporters: TC-DB (Microbiol Mol Biol Rev. 64:354-411)

 

Protein family prediction methods:

  • Multiple sequence alignments. JMB 235, 1501-153 (1994); JMB 301, 173-190.
  • Neural network: ProtFun. J. Mol. Biol. 319:1257-1265, (2002)
  • Support vector machines: SVMProt. Nucleic Acids Res., 31: 3692-3697 (2003)

 

Sequence alignment:

  • Needleman-Wunsch method: JMB 48, 443-453 (1970)
  • PAM: A model of evolutionary change in proteins. In: Atlas of protein sequence and structure (Natl. Biomed. Res. Found. Washington) Vol 5, Suppl 3. pp.345-358 (1978).
  • Smith-Waterman method: JMB 147, 195-197 (1981)
  • FASTA: Proc. Natl. Acad. Sci. USA 85, 2444 (1988)
  • BLAST: JMB 215, 403-410 (1990).
  • BLOSUM: Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
  • HMM: JMB 235, 1501-153 (1994)

 

Support vector machines:

  • C. Burges, "A tutorial on support vector machines for pattern recognition", Data Mining and Knowledge Discovery, Kluwer Academic Publishers,1998 (on-line).
  • R. Duda, P. Hart, and D. Stork, Pattern Classification, John-Wiley, 2nd edition, 2001 (section 5.11, hard-copy).
  • S. Gong et al. Dynamic Vision: From Images to Face Recognition, Imperial College Pres, 2001 (sections 3.6.2, 3.7.2, hard copy).

 

Protein structure

  • SCOP  database. J. Mol. Biol. 247, 536-540

 

Molecular modelling:

  • AMBER: J. Am. Chem. Soc. 117, 5179-5197
  • CHARMM: J. Comp. Chem. 4, 187-217
  • Hydrogen bond model and parameters: Nucleic Acids Res. 20, 415-419. Biophys. J. 66, 820-826
  • Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein nucleic acid noncovalent interactions. Annu. Rev. Biophys. Biomol. Struct. 30, 211-243 (2001).

 

Protein structure prediction methods:

  • Protein folding theory: From lattice to all-atom models. Annu. Rev. Biomol. Struct. 30, 361-396 (2001).
  • Knowledge-based protein modelling. Critical Rev. Biochem. Mol. Biol. 29, 1-68 (1994).
  • Comparative protein structure modelling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325 (2000).
  • Ab initio protein structure prediction: Progress and prospects. Annu. Rev. Biophys. Biomol. Struct. 30, 173-189.

 

Biological pathway databases:

 

Pathway simulation methods:

  • Dynamic biochemical reaction process analysis and pathway modification predictions. Biotechnol. Bioeng. 68, 285-297 (2000)
  • A mathematical model of caspase function in apoptosis. Nature Biotech. 18, 768-774 (2000)

   
           
 
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