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 and the MMTSB Tool Set" (July 31 - August 4, 2006). Participants are urged to review the papers prior to your arrival.

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.