next up previous
Up: Parameterization Tutorial Previous: Minimization with new parameters


MacKerell et. al.
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
J. Phys. Chem. B, 102:3586-3616, 1998.

Jr. A.D. MacKerell and N. Banavali.
All-atom empirical force field for nucleic acids: 1) parameter optimization based on small molecule and condensed phase macromolecular target data.
J. Comp. Chem., 21:86-104, 2000.

J. Wang, P. Cieplak, and P.A. Kollman.
How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules.
J. Comp. Chem., 21:1049-1074, 2000.

W. Jorgensen, S. Maxwell, and J. Tirado-Rives.
Development and testing of the opls all-atom force field on conformational energetics and properties of organic liquids.
J. Amer. Chem. Soc., 117:11225-11236, 1999.

C. Rizzo and W. Jorgensen.
Opls all-atom model for amines: Resolution of the amine hydration problem.
J. Amer. Chem. Soc., 121:4827-4836, 1999.

Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, and Zaida Luthey-Schulten.
Classical force field parameters for the heme prosthetic group of cytochrome c.
J. Comp. Chem., 25:1613-1622, 2004.

A. Mackerell.
Parametrization of molecules for use of charmm., 2003.

A. Mackerell.
Workshop on methods and applications of molecular dynamics to biopolymers., 2003.

J. Wang, R.M. Wolf, J. Caldwell, P. Kollman, and D. Case.
Development of a general amber force field., 2003.

P. Pulay, G. Fogarasi, F. Pang, and J.E. Boggs.
Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives.
J. Amer. Chem. Soc., 101:2550-2560, 1979.

H. Stern, G.A. Kaminski, J.L. Banks, R. Zhou, B.J. Berne, and R.A. Friesner.
Fluctuating charge, polarizable dipole, and combined models: parametrization.
J. Phys. Chem. B, 103:4730-4737, 1999.

W. Humphrey, A. Dalke, and K. Schulten.
Vmd - visual molecular dynamics.
J. Mol. Graph., 14:33-38, 1996.

Inc. Wavefunction.
Spartan '02 tutorial and user's guide.
Irvine, CA, 2001.

B. Chaudhuri, S. Lange, S. Chittur R. Myers, V. Jo Davisson, and J. Smith.
Crystal structure of imidazole glycerol phosphate synthase: A tunnel through a (beta-alpha)8 barrel joins two active sites.
Structure, 9:987-997, 2001.

A. Douangamath, M. Walker, S. Beismann-Driemeyer, M. Vega-Fernandez, R. Sterner, and M. Wilmanns.
Structural evidence for ammonia tunneling across the (beta-alpha)8 barrel of imidazole glycerol phosphate synthase bienzyme complex.
Structure, 10:185-193, 2002.

Barnali N. Chaudhuri, Stephanie C. Lange, Rebecca S. Myers, V. Jo Davisson, and Janet L. Smith.
Toward understanding the mechanism of the complex cyclization reaction catalyzed by imidazole glycerolphosphate synthase: Crystal structures of a ternary complex and the free enzyme.
Biochemistry, 42:7003 - 7012, 2003.

P. O'Donoghue, R. Amaro, and Z. Luthey-Schulten.
On the structure of hish: Protein structure prediction in the context of structural and functional genomics.
J. Struct. Bio., 134:257-268, 2001.

R. Amaro, E. Tajkhorshid, and Z. Luthey-Schulten.
Developing an energy landscape for the novel function of a (beta-alpha)8 barrel: Ammonia conduction through hisf.
Proc. Natl. Acad. Sci., 100:7599-7605, 2003.

T Klem and V Davisson.
Imidazole glycerol phosphate synthase: The glutamine amidotransferase in histidine biosynthesis.
Biochemistry, 32:5177-5186, 1993.

T. J. Klem, Y. Chen, and V. J. Davisson.
Subunit interactions and glutamine utilization by Escherichiacoli imidazole glycerol phosphate synthase.
J Bacteriol, 183:989-996, 2001.

J. Thoden, S. Miran, J. Phillips, A. Howard, F. Raushel, and H. Holden.
Carbamoyl phosphate synthetase: Caught in the act of glutamine hydrolysis.
Biochemistry, 37:8825-8831, 1998.

Rommie Amaro and Zaida Luthey-Schulten.
Molecular dynamics simulations of substrate channeling through an alpha-beta barrel protein.
Chem. Phys., 307:147-155, 2004.

D. Zacharias, P. Murray-Rust, R. Preston, and J. Glusker.
The geometry of the thioester group and its implications for the chemistry of acyl coenzyme a.
Archives of Biochemistry and Biophysics, 222:22-34, 1982.