Brookes

The Electronic Future for Managing Ship Condition Data", 1997, Dr K Brook... 

Brooks F C 1952 Convergence of intermolecular force series Phys. Rev. 86 92... 

Brooks H, Birch F, Hoiton G and Paui W (eds) 1964 Collected Experimental Papers of PW Bridgman voi i-Vii (Cambridge Harvard University Press)... 

C. Brooks III, M. Karplus, and B. Pettier, Proteins. A theoretical perspective of dynamics, structure, and thermodynamics, John Wiley Sons, Inc., New York, 1988, also Adv. Chem. Phys. LXXI,... 

Brooks III, C.L., Karplus, M. Deformable stochastic boubdaries in molecular dynamics. J. Chem. Phys. 79 (1983) 6312-6325. 

Loncharich, R.J., Brooks, B.R. The effects of truncating long-range forces on protein dynamics. Proteins 6 (1989) 32 5. 

Hayward et al. 1994] Hayward, S., Kitao, A., Go, N. Harmonic and anharmonic aspects in the dynamics of BPTI A normal mode analysis and principal component analysis. Prot. Sci. 3 (1994) 936-943 [Head-Gordon and Brooks 1991] Head-Gordon, T., Brooks, C.L. Virtual rigid body dynamics. Biopol. 31 (1991) 77-100... 

Bernhard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, and Martin Karplus. CHARMM A program for macro-molecular energy, minimization, and dynamics calculations. J. Comp. Chem., 4(2) 187-217, 1983. 

Charles L. Brooks III, B. Montgomery Pettitt, and Martin Karplus. Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids. J. Chem. Phys., 83(ll) 5897-5908, December 1985. 

E. M. Boczko and C. L. Brooks III. First principles calculation of the folding free energy of a three helix bundle protein. Science, 269 393-396, 1995. 

For future reference, the Verlet algorithm [18] can be generalized to iticlude the friction and stochastic terms above, and is typically used in the following form described by Brooks, Briinger and Karplus, known as BBK [23, 37] ... 

A. Briinger, C. L. Brooks, III, and M. Karpins. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett., 105 495-500, 1982. 

R. J. Loncharich, B. R. Brooks, and R. W. Pastor. Langevin dynamics of peptides The frictional dependence of isomerization rates of N-acetylalanyl-N -methylamide. Biopolymers, 32 523-535, 1992. 

P. Derreumaux, G. Zhang, B. Brooks, and T. Schlick. A truncated-Newton method adapted for CHARMM and biomolecular applications. J. Comp. Chem., 15 532-552, 1994. 

B. R. Brooks and M. Karplus. Normal modes for specific motions of macromolecules Application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA, 82 4995-4999, 1985. 

Brooks, B. R., Janezic, D., Karplus, M. Harmonic Analysis of Large Systems I. Methodology. J. Comput. Chem. 16 (1995) 1522-1542 Janezic, D., Brooks, B. R. Harmonic Analysis of Large Systems II. Comparison of Different Protein Models. J. Comput. Chem. 16 (1995) 1543-1553 Janezic, D., Venable, R. M., Brooks, B. R. Harmonic Analysis of Large Systems. HI. Comparison with Molecular Dynamics. J. Comput. Chem. 16 (1995) 1554-1566... 

Watanabe, M., Karplus, M. Dynamics of Molecules with Internal Degrees of Freedom by Multiple Time-Step Methods. J. Chem. Phys. 99 (1995) 8063-8074 Figueirido, F., Levy, R. M., Zhou, R., Berne, B. J. Large Scale Simulation of Macromolecules in Solution Combining the Periodic Fast Multiple Method with Multiple Time Step Integrators. J. Chem. Phys. 106 (1997) 9835-9849 Derreumaux, P., Zhang, G., Schlick, T, Brooks, B.R. A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. J. Comp. Chem. 15 (1994) 532-555... 

Brooks III, C. L., Karplus, M., Pettitt, B. M. Proteins A Theoretical Perspective of Dynamics, Structure and Thermodynamics. Advances in Chemical Physics, vol. LXXI. John Wiley Sons, New York, 1988. 

Y. Hwang, R. Das, F. H. Saltz, M. Hadoscek and B. R. Brooks, Parallelizing molecular dynamics programs for distributed-memory machines , IEEE Computational Science and Engineering, Vol 2, no 2, 18-29, 1995. 

Brooks [II, ( L. Kirphis. M. Pcuill, B.M. Proteins A I heoreiiral Perspective of Dynamics, Struc.lure, and Phemiodynam ics, in Advances in Che.mioal Physios. Vol. 7 1. John Wiley iind Son s. New York, 1 9HS. 

CIIARMM was first developed as a united atom force field and parameters for some amino acids have been published B. R. Brooks et al.. 1 Comp. ( hem.. 4, 1H7 fl9K3). Siihseqiient changes to the functional form and param eters h ave been published W. Reiher, Ph.D.. TIarvard but most recent parameter develop-... 

Brooks B and M Karplus 1983. Harmonic Dynamics of Proteins Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor. Proceedings of the National Academy of Sciences USA 80 6571-6575. 

Brunger A, C B Brooks and M Karplus 1984. Stochastic Boundary Conditions for Molecular Dynaniii Simulations of ST2 Water. Chemical Physics Letters 105 495-500. 

Fleischman S H and C L Brooks III 1987. Thermodynamics of Aqueous Solvation - Solution Properties of. Mcohols and Alkanes. Journal of Chemical Physics 87 3029-3037. 

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