MMTSB/CTBP Workshop Reading List

Reading materials

The following list of papers provides recommended background reading for the MMTSB/CTBP Summer Workshop "Molecular simulation and structure prediction using CHARMM, Amber and the MMTSB Tool Set" (August 4-7, 2009). Participants are urged to review the papers prior to your arrival.

The CHARMM Program

  • CHARMM: The Biomolecular Simulation Program. B.R. Brooks, C.L. Brooks III, A.D. MacKerell, Jr., L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schefer, B. Tidor, R.M. Venable, H.L. Woodcock, X. Wu, W. Yang, D.M. York, M. Karplus. J Comput Chem 30: 1545-1614, 2009.
  • Force Fields

  • Empirical Force Fields for Biological Macromolecules: Overview and Issues. Alexander D. MacKerell, Jr. J Comput Chem 25: 1584-1604, 2004.
  • CHARMM Fluctuating Charge Force Field for Proteins: II Protein/Solvent Properties from Molecular Dynamics Simulations Using a Nonadditive Electrostatic Model. Sandeep Patel, Alexander D. MacKerell, Jr. and Charles L. Brooks III. J Comput Chem 25: 1504-1514, 2004.
  • Implicit solvent - Generalized Born and Poisson Boltzmann

  • Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models. Wonpil Im, Jianhan Chen and Charles L. Brooks III. Adv Prot Chem 72: 173-198, 2006.
  • A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes. Seiichiro Tanizaki and Michael Feig. J Chem Phys 122: 124706, 2005.
  • Theoretical and computational models of biological ion channels. Benoìt Roux, Toby Allen, Simon Bernèche and Wonpil Im. Quart Rev Biophys 37: 15-103, 2004.
  • MMTSB Tool Set

  • MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. Michael Feig, John Karanicolas and Charles L. Brooks III. J Molec Graph Modl 22: 377-395, 2004.
  • Applications

  • Computational Approaches for Investigating Base Flipping in Oligonucleotides. U. Deva Priyakumar and Alexander D. MacKerell, Jr. Chem Rev. 106: 489-505, 2006.
  • Molecular Dynamics Simulations of Large Integral Membrane Proteins with an Implicit Membrane Model. Seiichiro Tanizaki and Michael Feig. J Phys Chem B. 110: 548-556, 2006.
  • Extending the Horizon: Towards the Efficient Modeling of Large Biomolecular Complexes in Atomic Detail. Michael Feig, Jana Chocholousova, Seiichiro Tanizaki. Theoretical Chemistry Accounts, 2006.
  • Minimalist (Go) Models

  • The origins of asymmetry in the folding transition states of protein L and protein G. John Karanicolas and Charles L. Brooks III. Prot Sci. 11: 2351-2361, 2002.
  • Amber references

  • Computational Chemistry and Biophysics O.M. Becker, A.D. MacKerrell, Jr., B. Roux, M. Watanabe, eds, Marcel Dekker, 2001: Chapter 3 "Dynamics Methods" pp39-67
  • D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. "The Amber biomolecular simulation programs". J. Computat. Chem. 26, 1668-1688 (2005).
  • R.C. Walker, M.F. Crowley, D.A. Case, "The Implementation of a Fast and Accurate QM/MM Potential Method in Amber.", J. Comput. Chem. 29, 1019-1031 (2008)

  • Y. Sugita, Y. Okamoto, "Replica-exchange molecular dynamics method for protein folding.", Chem. Phys. Lett., 314, 141-151 (1999)