SI2011 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 C/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: Robert Konecny, Ph.D., Gary Huber, Ph.D., Pete Kekenes-Huskey, Ph.D.

Time: M-F, 9:00 am to 12 pm, Aug 1-5, 2011

Location: Atkinson Hall, Room 3004, Building 603

Prerequisite Basic UNIX knowledge required. Some scripting (Python, Perl, bash, etc.) background helpful. Math background important (at least calculus, ideally differential equations). Also, all participants are required to bring their own laptop, preferably less than 2 years old with a good graphics card.

Software Requirements

  • Required software
  • Optional software
    • AMBER (for optional labs)

Study Materials


  • Monday, Tuesday: Computational electrostatics for biomolecular systems
    Instructor: Robert Konecny, Ph.D. Online tutorial
  • Wednesday: Brownian dynamics and coarse-grained modeling
    Instructor: Gary Huber, Ph.D. BrownDye
  • Thursday: Continuum diffusion modeling using the C/SMOL package
    Instructor: Pete Kekenes-Huskey, Ph.D. SMOL Lecture notes
  • Friday: Case studies and Advanced topics
    Instructor: All.

Related Tracks from Previous SI

SI2010 Molecular Electrostatics and Diffusion

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