References
Please cite the following as references to SDA 7:

Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, Öztürk MA, Richter S, Wade RC.
SDA7: A Modular and Parallel Implementation of the Simulation of Diffusional Association Software.  J. Comput. Chem. (2015) 36, 1631-1645. (doi)
Gabdoulline RR and Wade RC.
Brownian Dynamics Simulation of Protein-Protein Diffusional Encounter.  Methods (1998) 3, 329-341. (doi, Citations)
Gabdoulline RR and Wade RC.
Simulation of the Diffusional Association of Barnase and Barstar.  Biophys. J. (1997) 72, 1917-1929. (Abstract, Citations)
Describe the SDA method

Gabdoulline RR and Wade RC.  Effective charges for Macromolecules in Solvent.  J. Phys. Chem. (1996) 100, 3868-3878. (doi, Citations)
 Describes the ECM method

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. (doi, Citations)
Describes the electrostatic desolvation term

Reinhardt M, Bruce NJ, Kokh D, Wade RC. Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-range Electrostatics and Mean-Field Hydrodynamics

Gabdoulline RR and Wade RC .  On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f : Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events.   J. Am. Chem. Soc. (2009) 131, 9320-9238. (doi, Citations)
Describes the nonpolar desolvation term

Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, and Wade RC .  ProMetCS: an atomistic force field for modeling protein-metal surface interactions in a continuum aqueous solvent.   J. Chem. Theor. Comput. (2010) 6, 1753-1768, . (doi, Citations)
Describes the ProMetCS model of protein-metal interactions

Mereghetti P, Gabdoulline R, and Wade RC.  Brownian dynamics simulation of protein solutions: Structural and dynamical properties.   Biophys. J. (2010) 99, 3782-3791 . (doi, Citations)
Describes the simulation of multiple protein molecules with SDA

Mereghetti P, and Wade RC.  Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.   J. Phys. Chem. B. (2012) 116, 8523-8533 . (doi, Citations)
Describes the mean field treatment of hydrodynamic interactions in simulations of concentrated protein solutions with SDA

Mereghetti P, Martinez M, and Wade RC.  Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules.   BMC Biophysics. (2014) 7:4 . (doi, Citations)
Describes the Debye-Hückel approximation at large distance in simulations of concentrated protein solutions with SDA

Ozboyaci M, Martinez M, and Wade RC.  An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association   JCTC (2016), 59, 7598-7616.  DOI: 10.1021/acs.jctc.6b00350
Describes the implementation of the dynamic tubular grid representation of interaction potential grids.

Some references describing applications (list not updated)

  1. Harel, M., Spaar, A. and Schreiber G. Fruitful and Futile Encounters along the Association Reaction between Proteins . Biophys. J. (2009) 96, 4237-4248. (Citations)

  2. Spaar, A., Floeck, D. and Helms V. Association of Cytochrome c with Membrane-Bound Cytochrome c Oxidase Proceeds Parallel to the Membrane Rather Than in Bulk Solution . Biophys. J. (2009) 96, 1721-1732. (Citations)

  3. Feldman-Salit, A., Wirtz, M., Hell, R. and Wade RC. A mechanistic model of the cysteine synthase complex . J. Mol. Biol. (2009) 386, 37-59. (Citations)

  4. Motiejunas D, Gabdoulline RR, Wang T, Feldman-Salit A, Johann T, Winn PJ, Wade RC. Protein-protein docking by simulating the process of association subject to biochemical constraints. Proteins (2008) 71, 1955-1969. (Citations)

  5. Pachov G,  Gabdoulline RR, Wade RC. Simulation of Linker Histone-Chromatin Interactions. In  "From Computational Biophysics to Systems Biology (CBSB2007)", John von Neumann Institute for Computing, Juelich | NIC Series (2007) 36,  69-74. (Citations)

  6. Blachut-Okrasinska E and Antosiewicz JM. Brownian Dynamics Simulations of Binding mRNA Cap Analogues to eIF4E Protein. J. Phys. Chem. B (2007) 111 (45), 13107-15. (doi, Citations)

  7. Spaar A, Dammer C, Gabdoulline RR, Wade RC and Helms V. Diffusional encounter of barnase and barstar.  Biophys. J. (2006) 90, 1913-1924. (Abstract, Citations)

  8. Spaar A and Helms V.  Ionic strength effects on the association funnel of barnase and barstar investigated by Brownian dynamics simulations. J. Non-Crystalline Solids (2006) 352,(42-49):4437-44. (doi, Citations)

  9. 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. (doi, Citations)

  10. 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. (Abstract, Citations)

  11. 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. (Abstract, Citations)

  12. Sun J, Viadiu H, Aggarwal AK and Weinstein H. Energetic and Structural Considerations for the Mechanism of Protein Sliding along DNA in the Nonspecific BamHI-DNA Complex.  Biophys J. (2003) 84(5): 3317–25. (Abstract, Citations)

  13. 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. (Abstract, Citations)

  14. Elcock AH. Atomistic Simulations of Competition between Substrates Binding to an Enzyme. Biophys J (2002) 82(5):  2326-32. (Abstract, Citations)

  15. Gabdoulline RR and Wade RC. Biomolecular diffusional association. Curr. Opin. Struct. Biol. (2002) 12, 204-213. (doi, Citations)

  16. 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. (Abstract, Citations)

  17. 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. (Abstract, Citations)

  18. 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. (doi, Citations)

  19. 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. (doi, Citations)

  20. ElcockAH, Gabdoulline RR, Wade RC and McCammon JA.  Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin.  J. Mol. Biol. (1999) 291, 149-162. (doi, Citations)

  21. Gabdoulline RR and Wade RC.  On the Protein-Protein Diffusional Encounter Complex.  J. Mol. Recogn. (1999) 12, 226-234. (Abstract, Citations)

  22. Gabdoulline RR and Wade RC.  Brownian Dynamics Simulation of Protein-Protein Encounter.  Methods (1998) 3, 329-341. (doi, Citations)

  23. 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. (Link, Citations)

  24. Gabdoulline RR and Wade RC.  Simulation of the Diffusional Association of Barnase and Barstar.  Biophys. J. (1997) 72, 1917-1929. (Abstract, Citations)

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