Reading List

Biophysics 298:  Computation of Biological Molecules, Winter 2003

Instructor:  Matt Jacobson [matt@cgl.ucsf.edu]

 

This course is really set up so that you can get as much out of it as you wish.  You’ll learn a lot simply by showing up and listening; you’ll learn more if you at least skim some of the readings below, which include both primary and secondary sources, before the class session.  If you are in charge of presenting a topic, you will likely want to read all of the sources listed for it, and probably others. 

 

No specific textbook is required.  I know that many of you already own the 1st or 2nd edition of Molecular Modelling (A. R. Leach), which provides an overview of many topics.  The new textbook Molecular Modeling and Simulation by Tamar Schlick is another alternative, particularly strong on algorithmic issues.  Allen and Tildesley, Computer Simulation of Liquids, provides a good introduction to simulation methods, although of course it does not explicitly deal with macromolecules. 

 

I also recommend the Encyclopedia of Computational Chemistry (referred to as ECC below) for useful, concise overviews and references.  Unfortunately, the campus library does not appear to own a copy, but there is a copy in the "library" inside the U80 complex.  Please do not remove it from this room.

 

The list of primary sources is incomplete and will grow during the quarter.  Given the vastness of the literature, my goal is not to provide an exhaustive bibliography, but simply to provide a few articles that provide a useful overview of a particular topic, are historically important, and/or are especially clear or otherwise didactically useful.  Since most recent journal articles are available online, I provide hyperlinks here (through UCSF’s electronic journal subscriptions), to create a "virtual course reader".  Some older articles are available only in print; I plan to photocopy and distribute certain of these articles, as appropriate.  Non-journal web-based resources are also becoming increasingly important sources of information, and a few are also referenced below. 

 

 

Topic 2.1:  Fixed charge force fields.

·        Leach, 1st Ed.:  Sections 3.1-3.7, 3.9, 3.12, 3.14 (not 3.14.1), 3.15-3.18.

·        Leach, 2nd  Ed.:  Section 4.1-4.6, 4.10, 4.13, 4.15 (not 4.15.1), 4.16, 4.18, 4.19.

·        Schlick:  Sections 7.2.6, 7.3, 7.4, 8.2.3, 8.3-8.8. 

·        ECC articles:  "AMBER", "CHARMM", "Force fields:  A brief introduction", "Force fields:  A general discussion", "ECEPP", "GROMOS", "OPLS", "Protein force fields".

·        A. D. MacKerell, Jr. et al.  "All-atom empirical potential for molecular modeling and dynamics studies of proteins".  JPCB 102 (1998) 3586-3616.  Online

·        W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives.  "Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids".  JACS 118 (1996) 11225-11236.  Online

·        W. D. Cornell et al.  "A second generation force field for the simulation of proteins nucleic acids, and organic molecules".  JACS  117 (1995) 5179-5197.  Online

·        Online resources:  AMBER home page.

 

Topic 2.2:  Polarizable force fields.

 

Topic 2.3:  Atom-typing and partial charges.

 

Topics 3 & 4:  Good general references on water simulations and relevance to biology.

 

Topic 3.1:  Explicit water models.

 

Topic 3.2:  Periodic boundary conditions.

 

Topic 3.3:  Non-periodic boundary conditions.

 

Topic 3.4:  Predicting buried waters in proteins.

 

Topic 4.1:  Poisson-Boltzmann.

 

Topic 4.2:  Generalized Born.

·        Leach, 1st Ed.:  Section 9.9.2.

·        Leach, 2nd  Ed.:  Section 11.10.2.

·        W. C. Still et al.  "Semianalytical treatment of solvation for molecular mechanics and dynamics".  JACS 112 (1990) 6127-6129.  Online

·        A. Ghosh, C. S. Rapp, and R. A. Friesner.  "Generalized Born model based on a surface integral formulation".  JPCB  102 (1998) 10983-10990.  Online

·        A. Onufriev, D. Bashford, and D. A. Case.  "Modification of the Generalized Born model suitable for macromolecules".  JPCB  104 (2000) 3712-3720.  Online

·        B. N. Dominy and C. L. Brooks, III.  "Development of a Generalized Born model parameterization for proteins and nucleic acids".  JPCB 103 (1999) 3765-3773.  Online

 

Topic 4.3:  Hydrophobic solvation.

 

Topic 4.4:  Heuristic solvent models.

·        Leach, 1st Ed.:  Sections 3.8.11, 9.11.

·        Leach, 2nd  Ed.:  Sections 4.9.11, 11.12.

·        F. Fraternali and W. F. van Gunsteren.  "An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution".  JMB 256 (1996) 939-948.  Online

·        T. Ooi et al.  "Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides".  PNAS  84 (1987) 3086-3090.  Online

 

Topic 5.1:  Integrating Newton’s equations of motion.

 

Topic 5.3:  Approximate dynamics methods.

 

Topic 6.1:  Introduction to Monte Carlo sampling.

 

Topic 6.2:  Direct minimization.

 

Topic 6.3:  Global optimization.

 

Topic 7.1:  Analysis of trajectories.

 

Topic 7.2:  Applications to proteins/peptides.

 

Topic 7.3:  Free energy methods.

 

Topic 8:  QM/MM

 

Topic 9.1:  Model building from experimental data.

 

Topic 9.2:  Side chain optimization.

 

Topic 9.3:  Loop optimization.

 

Topic 9.4:  Homology model construction and refinement.

 

Topic 10.1:  Small molecule ligand docking: the role of all-atom energy functions.

 

Topic 10.3:  Protein-nucleic acid interactions.