SI2009 Molecular Electrostatics and Diffusion

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General Information

The track is geared towards beginning to intermediate level graduate students and postdocs. Advanced users are strongly encouraged to inquire ahead of time regarding topics of interest.

Students will learn the electrostatics and molecular diffusion theories and applications in molecular interactions and the supramolecular complexes. The tools covered include APBS, BrownDye, SMOL, which are important in the determination of the binding rate constant of protein-ligand interaction, protein-protein complex formation, or enzyme-substrate reactions. They also have important implications in virtual screening and computer aided drug design.

Each session includes lectures and hands on exercises.

Projected Outcome By the end of the sessions, the students should be familiar with basic and intermediate level of knowledge of the software packages listed (APBS, BrownDye and SMOL), in modeling the formation of molecular to supramolecular complexes and the determination of binding rate constants. Advanced users may wish to exchange ideas with the instructors ahead of time.

Instructors: Nathan Baker, Ph.D., Robert Konecny, Ph.D., Gary Huber, Ph.D., Yuhui Cheng, Ph.D.

Time M-F, 9 am to 12 pm, Aug 3-7, 2009

Location EBU2, Room 239

Prerequisite Basic UNIX knowledge required. Some scripting (Python, Perl, bash, etc.) background helpful. Math background important (at least calculus, ideally differential equations).

Software Requirements

Study Materials


  • Wednesday: Brownian dynamics and coarse-grained modeling
    Instructor: Gary Huber, Ph.D.
  • Thursday: Continuum diffusion modeling using the SMOL package
    Instructor: Yuhui Cheng, Ph.D.
  • Friday: Case studies and Advanced topics
    Instructor: All.

Lab Information

  • To initialize the necessary software environment execute the following in your terminal window before starting the lab:
    . ~/../public/elstat/sourceme
  • APBS examples directory is located here:

Related Tracks from Previous SI

SI2008 Molecular Electrostatics and Diffusion

Back to SI2009 program

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