Jianhan Chen Research Group
Computational Biophysics and Biomaterials

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Essential readings on molecular modeling for serious professionals

Disclaimer: This is a heavily biased/incomplete list, as limited by my personal background, research interests and past learning experience. It only means to provide some reasonable entry points to the large body of existing literature on biomolecular modeling.

Review Articles

  • General MD methodologies
    • JCC Special Issue on MD Packages (Vol. 26 Issue 16);
    • Brooks et al., 2009 (PMID: 19444816; the updated CHARMM paper);
    • Hess et al., J. Chem. Theo. Comput. (2008) (GROMACS 4 paper);
    • Tuckerman and Martyna, J. Phys. Chem. B (2000);
    • Schlick et al., J. Comput. Phys. (1999);
    • Scheraga et al., 2007 (PMID: 17034338);

  • Force Fields (No, they were not created by God.)
    • MacKerell, 2004 (PMID: 15264253): CHARMM-central review with broader pespective
    • Ponder and Case, 2003 (PMID: 14631816): general overview of empirical force fields
    • Lazaridis and Karplus, 2000 (PMID: 10753811): with some discussion on statistical potentials.

  • Implicit Solvent
    • Simonson and Roux, 1999 (PMID: 17030302)
    • Bashford and Case, 2000 (PMID: 11031278)
    • Feig and Brooks, 2004 (PMID: 15093837); an update, Chen et al., 2008 (PMID: 18304802);

  • Free Energy Methods
    • Case and Brooks, Chem. Rev. (1993);
    • Kollman, Chem. Rev. (1993);
    • Kumar et al., J. Comput. Chem. (1992,1995) (the original WHAM paper and multidimensional extension);
    • Gilson et al., Biophys. J. (1997) (almost all to be known about binding affinity calculations);
    • Allen et al., 2006 (PMID 16500984: ; ion channel PMF)
Books on Related Topics
  • "Understanding Molecular Simulations", by Frankel and Smit
  • "Computer Simulations of Liquids", by Allen and Tildesley
  • "Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics", by Brooks, Karplus and Pettitt
  • "Statistical Mechanics", by McQuarrie
  • "Introduction to Modern Statistical Mechanics", by David Chandler
Manuals of Your Favorite MD Programs (Yes, they are useful!)
  • CHARMM
  • Amber
  • NAMD/VMD
  • Gromacs
Want to add to the list? Please kindly let me know.

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