Documentation of program to
compute Boltzmann factor on encounter complexes
This version (4.23) of SDA
can be downloaded here.
Please note that the simulation program of the current distribution
expects the electrostatic and electrostatic desolvation grids to have
spacing equal to 1 A. You can change relevant force and energy routines
yourselves, to use not 1 A spacing grids, or request a patch from me.
References
Spaar A, Dammer C, Gabdoulline RR, Wade RC and Helms V.
Diffusional encounter of barnase and
barstar. Biophys. J. (2006) 90, 1913-1924.
Lin J and Beratan DN. Simulation of electron transfer between
cytochrome c2 and the bacterial photosynthetic reaction center:
Brownian dynamics analysis of the native protein and double mutants. J.
Phys. Chem. B(2005), 109,
7529-7534.
Flöck D, Helms V. A Brownian dynamics study: the
effect of a membrane environment on an electron transfer system. Biophys J. (2004)
87(1):65-74.
Wang T, Tomic S, Gabdoulline RR, Wade RC. How optimal are the
binding energetics of barnase and barstar? Biophys J. (2004) 87(3):1618-30.
Gabdoulline RR, Kummer U, Olsen LF, Wade RC. Concerted
simulations reveal how peroxidase compound III formation results in
cellular oscillations. Biophys J. (2003) 85(3):1421-8.
Elcock AH and McCammon JA. Calculation of weak protein-protein
interactions: The pH
dependence of the second virial coefficient. Biophys J. (2001) 80(2): 613-25.
De Rienzo F, Gabdoulline RR, Menziani MC, De Benedetti
PG and Wade RC. Electrostatic Analysis and Brownian Dynamics
Simulation of the Association of Plastocyanin and Cytochrome F.
Biophys. J. (2001) 81, 3090-3104.
Gabdoulline RR and Wade RC.
Protein-protein Association:
Investigation of Factors Influencing Association Rates by Brownian
Dynamics Simulations. J. Mol. Biol. (2001) 306, 1139-1155.
Elcock AH, Gabdoulline RR, Wade RC and McCammon JA.
Computer Simulation of Protein-Protein Association Kinetics:
Acetylcholinesterase-Fasciculin. J. Mol. Biol. (1999) 291,
149-162.
Gabdoulline RR and Wade RC. On the Protein-Protein
Diffusional Encounter Complex. J. Mol. Recogn. (1999) 12,
226-234.
Sept D, Elcock AH and McCammon JA.
Computer Simulation of Actin Polymerization Can Explain the
Barbed-Pointed
Asymmetry. J.Mol.Biol. (1999) 294, 1181-1189.
Gabdoulline RR. and Wade RC. Brownian Dynamics Simulation
of Protein-Protein Encounter. In "Computer Simulations and
Molecular Modeling Approaches to Biological Systems: Concepts and
Applications", Methods (1998) 3, 329-341.
Madura JD, Briggs JM, Wade RC and Gabdoulline RR.
Brownian Dynamics. In "Encyclopedia of Computational
Chemistry''. Eds. Schleyer PvR, Allinger NL, Clark T,
Gasteiger J, Kollman PA and Schaefer HF, Schreiner PR. John Wiley
& Sons: Chichester, UK, (1998) 1, 141-154.
Gabdoulline RR and Wade RC. Simulation of the
Diffusional Association of Barnase and Barstar. Biophys. J.
(1997) 72, 1917-1929.
Gabdoulline RR and Wade RC.
Effective charges for
Macromolecules in Solvent. J. Phys. Chem. (1996) 100, 3868-3878.