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  • Deprecated function: Using ${var} in strings is deprecated, use {$var} instead in include_once() (line 1442 of includes/bootstrap.inc).
  • Deprecated function: Using ${var} in strings is deprecated, use {$var} instead in include_once() (line 1442 of includes/bootstrap.inc).
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Introduction to MD simulation of DNA-protein systems
Tutorial PDF: 
PDF icon ssb-tutorial.pdf
Tutorial Files (link): 
Required tutorial files

This tutorial consists of five sections that gradually introduces the reader to Molecular Dynamics simulations as the skills and techniques needed to simulate the removal of ssDNA from single-stranded DNA binding protein are developed. The tutorial covers the basic of MD simulation,from the process of obtaining a protein model from the RCSB protein data bank to the analysis of steered MD data. Requires NAMD and VMD. Tutorial works on Mac and Unix/Linux platforms.

Example applications

  • Molecular mechanism of DNA association with single-stranded DNA binding protein
  • Molecular mechanism of DNA association with single-stranded DNA binding protein
  • Molecular mechanism of DNA association with single-stranded DNA binding protein