Track 2: Computer Aided Drug Discovery Pipeline

With abundant computing power available, computational studies have the opportunity to make unprecedented contributions to drug discovery efforts. Simulations are enabling routine incorporation of flexible receptor methodologies into drug discovery and design. Yet drug discovery is a process that involves multiple steps, many of which can be automated and aided by efficient computational approaches and pipeline.

Goal: By the end of the sessions, the participants should be able perform an ensemble-based virtual screen and analyze the results using the NBCR CADD pipeline. Users will learn how to apply molecular dynamics techniques within the context of the relaxed complex scheme and how such appraoches are being used to guide discovery and design of small molecule compounds.

Target Audience: The track is geared towards both beginning and intermediate level users of NAMD and AutoDock for the development of inhibitors to proteins and other validated pharmaceutical targets. Those interested in cheminformatics approaches in the post-processing of virtual screening results would also benefit. Those interested in the use of more advanced techniques in the evaluation of binding rate constant should consider the Molecular Electrostatics and Diffusion track.

Prerequisites: Students are expected to have:

  • Basic knowledge of structural biochemistry, cheminformatics and thermodynamics is a plus.
  • Familiarity with molecular dynamics theory and applications, such as NAMD, AMBER, GROMACS, or GROMOS, and with visualization programs such as PMV, VMD, or Molegro. We do encourage students to work through the VMD tutorial before attending (info below).
  • Students are required to bring their own laptop, with CADD pipeline and one of the visualization programs such as PMV or VMD preinstalled.
  • Students in the CADD Pipeline track are requested to work through the VMD tutorial on their own before classes start on Monday. This tutorial takes approximately 2 hours.
  • It will also be helpful if students work through the Using AutoDock4 with AutoDockTools Tutorial

Topics: Students will learn the basics of ensemble based docking, including (but not limited to): how to extract relevant structures via clustering or QR factorization; multiple receptor virtual screening; visualization; rescoring; hit analysis.

Format: Presentations and hands-on tutorials. This track will also have an afternoon lab for work on projects generated by the participant, with instructors helping to guide the projects advancement.

Course Materials

  • M-Th CSE 1202
  • Fr Fung Auditorium
  • M-F 9:00 - 12:00, July 30 - August 3
  • M-Th 14:00 - 17:00, July 30 - August 2
Victoria Feher, Ph.D.
Steffen Lindert, Ph.D.
Levi Pierce, Ph.D.
Jesper Sorensen, Ph.D.
Ying Su, Ph.D.
Robert Swift, Ph.D.
Jeff Wereszczynski, Ph.D.