Protein Modeling and Computational Chemistry
References

Abola, E. E., Bernstein, F. C., Bryant, S. H., Koetzle, T. F., and Weng, J.
 (1987) Protein Data Bank, in Crystallographic Databases - Information
 Content, Software Systems, Scientific Applications (F. H. Allen, G. 
 Bergerhoff * R. Sievers, eds.) Data Commission of the International 
 Union of Crystallography, Bonn, pp. 107-132.

Allen, F. H., Bellar, S., Brice, M. D., Cartwright, B. A., doubleday, A.,
 Higgs, H. Hummelink, T., Hummeling-Peters, B. G., Kennard, O., Motherwell,
 M. D. S., Rodgers, J. R., & Watson, D. G., (1979) The Cambridge 
 Crystallographic Datra Centre:  Computer-Based Search, Retrieval,
 Analysis and Display of Information, Acta Cryst. B35, 2331-2339.

Allinger, N. L. (1977) Conformational Analysis 130. MM2. A Hydrocarbon
 Force Field Utilizing V1 and V2 Torsional Terms, J. Am. Chem. Soc. 99,
 8127-8134.

Allinger, N. L., Kok, R. A., and Imam, M. R. (1988) Hydrogen Bonding in
 MM2, J. Comp. Chem. 9, 591-595.

Allinger, N. L., Yuh, Y. H., & Lii, J-H. (1989) Molecular Mechanics. 
 The MM3 Force Field for Hydrocarbons. 1.  J. Am. Chem. Soc. 111, 8551-8565.

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr.,
 Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tamusi,
 M. (1977) The Protein Data Bank: A Computer-based Archival File for
 Macromolecular Structures, J. Mol. Biol. 112, 535-542.

Besler, B. H., Merz, K. M., & Kollman, P. A. (1990) Atomic Charges Derived
 from Semiempirical Methods, J. Comp. Chem. 11, 431-439 (1990).

Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan,
 S., Karplus, M.  CHARMM:  A program for macromolecular energy, minmimization,
 and dynamics calculations.  J. Comp. Chem. (1983) 4, 187-217.

Burkert, U., & Allinger, N. L. (1982) Molecular Mechanics, American
 Chemical Society, Washington, DC.

Clark, M., Cramer III, R. D., van Opdenhosch, N., (1989) Validation of
 the General Purpose Tripose 5.2 Force Field, J. Comp. Chem. 10, 982-1012.

Dupuis, M., Spangler, D., & Wendoloski, J. J., (1980) Program QC01,
 National Resource for Computations in Chemistry Software Catalog,
 University of California, Berkeley, CA.

Dupuis, M., Watts, J. D., Villar, H. O., & Hurst, G. J. B., (1989a)
 The General Atomic and Molecular Electronic Structrue System: HONDO
 7.0, Comput. Phys. Comm. 52, 415- 425.

Dupuis, M., Mougenot, P., Watts, J. D., Hurst, G. J. B., & Villar,
 H. O.,(1989b) HONDO: A General Atomic and Molecular Electronic Structure
 System, in MOTECC: Modern Techniques in Computational Chemistry (E.
 Clementi, Ed.) ESCOM, Leiden, the Netherlands, pp. 306-361.

Frisch, M. G., Trucks, G. W., Head-Gordon, M., Gill, P. M. W., Wong, M. W.,
 Foresman, J. B., Johnson, B. G., Schlegel, H. B., Robb, M. A., Replogle,
 E. S., Gomperts, R., Andres, J. L., Raghavachari, K., Binkley, j. S.,
 Gonzalez, C., Martin, R. L., Fox, D. J., Defrees, D. J., Baker, J.,
 Stewart, J. J. P., & Pople, J. A., (1992)  Gaussian 92, Gaussian Inc.,
 Pittsburgh, PA.

Gibson, K. D.,  & Scheraga, H. A., (1986) Proc. natl. Acad. Sci. USA 83,
 5649-5653.

Hermans, J., Berendsen, H. J. C., van Gunsteren, W. F., & Postma, J.
 P. M., (1984) A Consistent Empirical Potential for Water- Protein
 Interactions, Biopolymers 23, 1513-1518.

Jorgensen, W. L., & Tirado-Rives, J.,(1988) The OPLS Potential Functions
 for Proteins. Energy Minimization for Crystals of Cyclic Peptides and
 Crambin, J. Am. Chem. Soc. 110, 1657- 1666.

Lii, J-H., Gallion,S., Bender,C., Wikstrom, H., Allinger, N. L., Flurchick,
 K. M., and Teeter, M. M.,(1989) Molecular Mechanics (MM2) Calculations
 on Peptides and on the Protein Crambin Using the Cyber 205, J. Comp.
 Chem. 10, 503-513.

Lii, J-H., & Allinger, N. L. (1989a) Molecular Mechanics.  The MM3 Force
 Field for Hydrocarbons. 2. Vibrational Frequencies and Thermodynamics,
 J. Am. Chem. Soc. 111, 8566-8575.

Lii, J-H., & Allinger, N. L. (1989b)  Molecular Mechanics.  The MM3 Force
 Field for Hydrocarbons. 3.  The van der Waals' Potentials and Crystal
 data for Aliphatic and Aromatic Hydrocarbons, J. Am. Chem. Soc. 111,
 8576-8582.

Lii, J-H., & Allinger, N. L. (1991) The MM3 Force Field for Amides,
 Polypeptides and Proteins, J. Comp. Chem. 12, 186- 199.

Mohamadi, F., Richards, N. G. J., Guida, W. C., Liskamp, R., Lipton,
 M., Caufield, C., Chang, G., Hendrickson, T., and Still, W. C., (1990)
 MacroModel- An Integrated Software System for Modeling Organic and
 Bioorganic Molecules Using Molecular Mechanics, J. Comp. Chem. 11, 440-467.

Momany, F. A., McGuire, R. F., Burgess, A. W., & Scheraga, H. A.,  (1975)
 Energy Parameters in Polypeptides VII, Geometric Parameters, Partial
 Charges, Non-bonded Interactions, Hydrogen Bond Interactions and
 Intrensic Torsional Potentials for Naturally Ocurring Amino Acids,
 J. Phys. Chem. 79, 2361-2381.

Momany, F. A., & Rone, R., (1992) Validation of the General Purpose
 QUANTA 3.2/CHARMm Force Field, J. Comp. Chem. 13, 888-900.

Mulholland, A. J., Grand, G. H. and Richards, W. G., "Computer Modeling
 of Enzyme Catalysed Reaction Mechanisms" Protein Engineering 6, 113-147
 (1993).

Nemethy, G., Pottle, M. S., & Scheraga, H. A., (1983) Energy Paramters
 in Polypeptides, 9. Updating of Geometrical Parameters, Non-bonding
 Interactions and Hydrogen Bonding INteractions for Naturally Occuring
 Amino Acids, J. PHys. Chem. 87, 1883-1887.

Pearlman, D. A., Case, D. A., Caldwell, J. C., Seibel, G. L., Singh,
 U. C., Weiner, P., & Kollman, P. A., (1991) AMBER 4.0, University
 of California, San Francisco.

Saenger, W. (1984) Principles of nucleic acid Structure., Springer-verlag,
 NY. (1984)

Sippl, M. J., Nemethy, G., & Scheraga, H. A.,  (1984) Intermolecular
 Potentials for Crystal Data 6. Determination of Empirical Potentials
 for 0-H---O=C Hydrogen Bonds for Packing Configurations, J. Phys.
 Chem. 88, 6231-6633.

Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Jensen, J. H., Koseki, S.,
 Gordon, M. S., Nguyen, K. A., Windus, T. L., & Gordon, M. S., (1990)
 QCPE Bulletin 10, 52-54.

Spellmeyer, D.C., Swope, W. C., & Evensen, E. R., (1989) San Francisco
 Package of Applications for the Simulation of Molecular Systems, Regents
 of the University of California, San Francisco, CA.

Stewart, J. J. P., (1990) J. Computer-Aided Mol. Des. 4, 1-105.

van Gunsteren, W. F., Berendsen, H. J. C., Hermans, J., Hole, W. G. J.,
 & Postma, J. P. M. (1983) Computer Simulation of the Dynamics of Hydrated
 Protein Crystals and Its Comparison with X-ray Data, Proc. Natl. Acad.
 Sci. USA, 80, 4315-4319.

Vedani, A., Dobler, M., Dunitz, J.D.  An empirical potential function
 for metal centers:  Application to molecular mechanics calculations
 on metalloproteins.  J. Comp. Chem. (1986) 7, 701-710.

Vedani, A.:  YETI:  An interactive molecular mechanics program for
 small-molecule protein complexes.  J. Comp. Chem. (1988) 9, 269-280.

Vedani, A., and Huhta, D. W.: A New Force Field for Modeling Metalloproteins.
 J. Am. Chem. Soc. (1990) 112, 4759-4767.

Weiner, P. K., & Kollman, P. A., (1981) AMBER: Assisted Model Building with
 Energy Refinement. A General Program for Modeling Molecules and Their
 Interactions, J. Comp. Chem. 2, 287-303.

Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona,
 G., Profeta, S., Jr., Weiner, P.K. (1984)  A new force field for molecular
 mechanical simulation of nucleic acids and proteins.  J. Am. Chem.
 Soc. 106, 765-784.

Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A., (1986)
 "An All Atom Force Field for Simulations of Proteins and Nucleic Acids,"
 J. Comp. Chem. 7, 230-252.