interaction-fingerprinting

There are many ways to improve structure-based virtual screening, from something as simple as screening the ligand based on the physico-chemical properties (MW, number of H-donor, number of aromatic rings, pKa, etc.), using consensus docking, or even post-analysis using FEP-based method. One of the simplest and yet fruitful approach to enhance the virtual screening workflow is using interaction fingerprinting. It has been known for long time that certain interaction from certain residue holds more significance than others....

What is a Domain-Specific Language? It is more common than you think. Few of us – computational chemists – have heard the term Domain-Specific Language (DSL for short), even though this is somewhat ubiquitous in our workflow, especially when dealing with molecule visualisation. Don’t you believe me? Check out the command you type on VMD, PyMOL, YASARA, or Chimera. YASARA command: LoadPDB 1crn, download=yes AutoPosOriObj 1, x = 1, y = 10, z = 0, alpha = 0, beta = 0, gamma = 0 ColorRes cys, green ShowRes cys BallStickRes cys AutoRotateObj 1, Y = 1 wait 180 AutoRotateObj 1, Y = 0 ZoomRes Cys 16, step = 50 wait 100 ZoomRes all VMD Tcl/Tk command:...