Difference Between Patchdock & Grammx

Question

[Pol]

Hello Friends,

What is the difference between online servers like PATCHDOCK & GRAMMX?

Answer 1

[João Rodrigues]

You should read their papers to find out the differences..

In short, from what I read, Patchdock doesn't seem to perform any kind of refinement on the generated complexes. It is based on shape complementarity and ranked on that alone. GRAMMX on the other hand, uses traditional FFT methods to generate initial structures and then apparently refines them for atomic clashes and gives you back a ranking based on a knowledge based scoring function. They are both doing what is known as "rigid body docking", therefore allowing for little or no flexibility.

Furthermore, you have plenty of other servers for protein-protein docking, some of which undergo several other steps and incorporate other features like flexibility, experimental data, etc... just a few: HADDOCK, RosettaDock, ZDOCK. You should select the server according also with the problem at hand.

Answer 2

[Payal]

patchdock is for protein-protein interaction and generates only a single best model whereas grammx generates many models.