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there is no need to run full rotation/translation search where one protein is rotated/
translated around the second protein structure. In most of the cases, there is no easy
way to define a proper boundary rotation and translation conditions; so the only way
is to carry out full search. However, in some cases, the user can define (usually with
complicated scripting) the instructions so that only rotations and translations within
membrane are possible. Naturally, one can also use the preexisting knowledge and
give to software predocked complex and ask the algorithm to carry out only local
docking and refinement. This option is typically easily available and also it will
speed up the computations remarkably.
Once all the files have been created, the actual docking run will be carried out.
The CPU time required for docking can vary a much, but at least 1-2 h is usually
needed.
5.1.3 Reliability
As stated earlier, scoring is the main problem when GPRC docking is carried out. To
overcome this, one should use all the possible empirical data. We have also devel-
oped an iterative approach to tackle the problem. In our approach, we apply protein-
protein docking with Rosetta software to obtain populations of dimers as present in
membranes with all possible interfaces (28 interfaces for a homodimer). As the num-
ber of possible interfaces is reasonably small, it is possible to carry out detailed local
docking to optimize each possible docking pose. At the next stage, consensus scoring
procedure according to (i) Rosetta score, (ii) surface of the dimer interface, (iii) polar
contribution to the dimer interface, (iv) fractal dimension of the dimer interface
( Kaczor et al., 2012 ), (v) evolutionary conservation score ( Ashkenazy, Erez,
Martz, Pupko, & Ben-Tal, 2010 ), (vi) shape complementarity, (vii) electrostatic
complementarity, (viii) potential energy, and (ix) free energy of binding is applied.
The best models are minimized, and the whole cycle is iteratively repeated until the
results converge to a consistent dimer formation.
We do not believe that any of the current protein-protein docking scoring func-
tions is capable of reliable predictions. This does not mean that protein-protein dock-
ing methods cannot be used, but one cannot claim that results can be used as such.
The situation is somehow analog to small-molecular docking where the so-called
consensus scoring has been used over a long period of time.
5.2 MD SIMULATION
Nowadays, MD is an important computational tool to study GPCRs in complex sys-
tems under native-like conditions at a molecular level. The part A aims to give a gen-
eral overview about the capability of MD simulation in GPCR research by
highlighting recent milestones, while part B provides insights into some technical
aspects. Part B is kept in a short format as a detailed description is provided in
the chapter 4 within this edition.
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