References for Further Studies
of Computational Tools for Metalloprotein Studies

Ab Initio Quantum Calculations of Biologically Relavent Structures & Complexes:
J-H. Lii & N. L. Allinger (1998), "Directional Hydrogen Bonding in the MM3 Force Field. II," J. Comp. Chem. 19, 1001-1016.

E. Magnusson & N. W. Moriarty (1993) "Computational Convergence of Electronic Structure Calculations of Transistion Metal Ligand Complexes," J. Comp. Chem. 14, 961-969.

J-M. Mouesca, J. L. Chen, L. Noodleman, D. Bashford, and D. Case (1994) J. Am. Chem. Soc. 116, 11898-11914.

J. E. Wampler (1995), "Electrostatic Potential Derived Charges for Enzyme Cofactors: Methods, Correlations, and Scaling for Organic Cofactors," J. Chem. Inform. Computer Sci. 35, 617-632.

Solvation energies from surface and volume calculations:
W. G. Richards, P. M. King, & C. A. Reynolds (1989) "Solvation effects," Protein Engineering 2, 319-327

A. A. Rashin & M. A> Bukatin (1994) "A view of thermodynamics of hydration emerging from continuum studies," Biophys. Chem. 51, 167-192

A. A. Rashin & K. Namboodiri (1987) "A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes," J. Phys. Chem. 91, 6003-6012.

D. J. Giesen, C. J. Cramer & D. G. Truhlar (1994) "Entropic contributions to free energies of solvation," J. Phys. Chem. 98, 4141-4147.

Physical docking:
D. J. Bacon & J. Moult (1992) "Docking by least squares fitting of molecular surface patterns," J. Mol. Biol. 225, 849-858.

R. M. Jackson & M. J. E. Sternberg (1995) "A continuum model for protein-protein interactions: applications to the docking problem," J. Mol. Biol. 250, 258-275.

F. Jiang & S. -H Kim (1991) "Soft docking: matching of molecular surface cubes," J. Mol. Biol. 219, 79-102.

Pedro N. L. Palma (1998), "Studies of Macromolecular Recognition and Prediction of Redox Properties of Metalloproteins," Doctoral Dissertation, Universidade Nova de Lisboa, Portugal.

B. K. Shoichet & I. D. Kuntz (1991) "Protein docking and complementarity," J. Mol. Biol. 221, 327-346.

Brownian dynamics:
S. H. Northrup (1994) "Hydrodynamic motions of large molecules," Current Opinion in Structural Biology 4, 269-274.

S. H. Northrup & H. P. Erickson (1992) "Kinetics of protein protein association explained by brownian dynamics computer- simulation," PNAS (USA) 89, 3338-3342.

Structure refinement using molecular mechanics:
P. K. Warme, N. Go & H. A. Scheraga (1972) "Refinement of X-ray data on proteins," J. Comp. Phys. 9, 303-317.

A. T. Brunger, M. Karplus & G. A. Petsko (1989) "Crystallographic refinement by simulated annealing," Acta Cryst. A45, 50-61.

M. Levitt & S. Lifson (1969) "Refinement of protein conformations using a macromolecular energy minimization procedure," J. Mol. Biol. 46, 269-279.

Homology modeling using molecular mechanics:
S. H. Bryant & C. E. Lawrence (1993) "An empirical energy function for threading protein sequence through the folding motif," Proteins 16, 92-112.

N. Srinivasan & T. L. Blundell (1993) "An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure," Protein Engineering 6, 501-512.

D. E. Stewart, P. K. Weiner & J. E. Wampler (1987) "Prediction of the structure of proteins using related structures, energy minimization and computer graphics," J. Mol. Graphics 5, 133-140.

Molecular Dynamics Driven Free Energy Calculations:
T. P. Straatsma (1996) "Free Energy by Molecular Simulation," from Reviews in Computational Chemistry vol. 9 (K. B. Lipkowitz & D. B. Boyd, eds.), VCH Publishers, Inc., New York, pp. 81-127.

W. F. van Gunsteren (1988) "The role of computer simulation techniques in protein engineering," Protein Engineering 2, 5-13.

D. L. Beveridge & F. M. DiCapua (1989) "Free energy via molecular simulation," in Ann. Rev. Biophys. Chem. 18, 431-92.

Hybrid calculations:
C. A. Reynolds (1990) "Theoretical electrode potentials and conformational energies of benzoquinones and naphthoquinones in aqueous solution," J. Am. Chem. Soc. 112, 7545-7551.