Track 3: Molecular Electrostatics and Diffusion

Electrostatics and molecular diffusion theories are important in applications in molecular interactions and the supramolecular complexes. Two important tools in this area, APBS and BrownDye, which are important in the determination of the binding rate constant of protein-ligand interaction, protein-protein complex formation, or enzyme-substrate reactions. These tools also have important implications in virtual screening and computer aided drug design.

Goal: 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), 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.

Target Audience: 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.

Prerequisites: 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.

Topics: Computational electrostatics for biomolecular systems, Brownian dynamics and coarse-grained modeling.

Format: Presentation and hands-on tutorials

Course Materials

Location: Atkinson Hall, room 6004
Time: 9:00 - 12:00, M-F July 30 - August 3  
Robert Konecny, Ph.D.
Gary Huber, Ph.D.