University of Maryland Baltimore County

Biochemistry 644 - Molecular Modeling - Spring Semester, 2002

Bibliography - Books -

• 1. "Dynamics of Proteins and Nucleic Acids" by J. A. McCammon and S. C. Harvey. Cambridge Univ. Press. 1987
• 2. ``Molecular Modeling: principles and applications'' by A. R. Leach publ. Longmans, 1996 [Good overview of molecular modeling with some biochemical applications.]
• 3. Daan Frenkel (Editor) and Berend Smit (Editor) ``Understanding Molecular Simulation : From Algorithms to Applications'' Academic Press (1996) [This covers the basic physical chemistry of Monte Carlo and molecular dynamics without specific bichemical applications.]
• 4. Molecular Mechanics across Chemistry'' by A.K. Rappe and C.J. Casewit (1997) University Science Books, Sausalito, CA [A broad view covering examples from organic chemistry, inorganic chemistry, proteins, DNA, pharmaceutical and polymer chemistry applications.]

Journals covering biochemical molecular modeling:

• J. Computational Chem. - covers details of methods
• J. Molecular Graphics
• Biopolymers - covers applications and some methods
• Biophysical Journal
• Journal of Computer-Aided Molecular Design
• Biochemistry and Journal of Molecular Biology contain some articles with significant molecular modeling content.

Specific Journal Articles

• 1. Brooks,BR; Bruccolerii,RE; Olafson,BD; States,DJ; Swaminathan,S; Karplus,M (1983): CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Computational. Chem. 4, 187-217.

  The fundamental description of the basis and syntax of the charmm molecular mechanics code

• 2. Weiner, P.K. and Kollman,PA (1981): Description of the AMBER program for molecular mechanics. J. Computational. Chem. 2, 287-303.

• 3. Weiner,SJ; Kollman,PA; Nguyen,DT; Case,DA (1986): All atom force field for simulations of proteins and nucleic acids. J. Computational. Chem. 7, 230- 252.

  This is the updated AMBER force field

• 4. Cornell,WD; Cieplak,P; Bayly,CI; Gould,IR; Mertz,KM; Ferguson,DM; Spellmeyer,DC; Fox,T; Caldwell,JW; Kollman,PA (1995): A second generation force field for the simulation of proteins, nucleic acids adn organic molecules. J. Amer. Chem. Soc. 117, 5179-5197.
• 5. Hagler,AT; Stern,PS; Sharon,R; Becker,JM; Naider,G (1979): Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results. J. Amer. Chem. Soc. 101, 6842-6852.
• 6. McCammon,JA (1987): Computer-aided Molecular Design. Science. 238, 486- 491.

  A Review of the thermodynamic cycle method for perturbative calculation of free energy changes for binding substrates to enzymes including site mutation effects. Brownian reactive dynamics described for use in calculating rates of diffusion controlled enzyme rates. AMBER and GROMOS are used in the dynamics simulation.

• 7. Harvey,SC (1989): Treatment of electrostatic effects in macromolecular modeling. Proteins: structure function and genetics 5, 78-92.

• 8. Brady,JW (1990): Molecular dynamics simulations of carbohydrate molecules. Adv. Biophys. Chem. 1, 155-202.

  Topics include the mol. dynamics simulations and conformational energy mapping of mono- and oligosaccharides.

• 9. Naidoo,Kevin J; Kuttel,Michelle (2001): Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations. J. Comput. Chem. 22(4), 445-456.

• 10. Liu,Q; Brady,JW (1997): Anisotropic solvent structuring in aqueous sugar solutions. J. Amer. Chem. Soc. 118, 12276-12286.

  Simulations with large water box for 3 solvent shells reported for xylose, lyxose and arabinose in both pyranoside forms. They report that differences in stereochemistry cause major differences in the solvent structure.

• 11. vanGunsteren,WF; Mark,AE (1992): On the interpretation of biochemical data by molecular dynamics computer simulation. Euro. J. Biochem. 204, 947- 961.

• 12. vanGunsteren,WF; Brunne,RM; Gros,P; vanSchaik,RC; Schiffer,CA; Torda, AE (1994): Accounting for molecular mobility in structure determination based on NMR spectroscopic and x-ray diffraction data. Methods in Enzymology 239, 619-653.

• 13. Field,MJ; Bash,PA; Karplus,M (1990): A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulation. J. Computational. Chem. 11, 700-733.

  Describes a hybrid quantum and classical mechanical scheme

• 14. Harvey,S.C. and Tan,R.K.Z. (1992): Teaching molecular modeling. Biophysical. Journal. 63, 1683-1688.

  Describes and evaluates a course in molecular modeling.

• 15. Metropolis,N; Rosenbluth,AW; Rosenbluth,MN; Teller,AH; Teller,E (1953): Equation of state calculations by fast computing machines. J. Chem. Phys.21, 1087-1092.

  This classic paper gives a simple description of the Metropolis algorithm for guided random searches for low energy conformations.

• 16. Wriggers,W; Mehler,E; Pitici,F; Weinstein,H; Schulten,K (1998): Structure and Dynamics of calmodulin in solution. Biophysical. Journal. 74, 1622-1639.

  Long 3 ns solution trajectory including counter ions shows motion of N and C domains from the crystal structure. Related to binding activity.>

• 17. Brunger,AT; Adams,PD; Clore,GM; DeLano,WL; Gros,P; Grosse-Kunstleve,RW; Jiang,JS; Kuszewski,J; Nilges,M; Pannu,NS; Read,RJ; Rice,LM; Simonson,T; Warren,GL (1998): Crystallography and NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. D54, 905-921.

  Describes the new CNS crystallography and NMR structure analysis program which replaces X-PLOR