I want to know at what default temperature docking is performed at easy interface? Is it performed at room temperature or between a temperature range? Because temperature is one of prime parameter, i want to know it.
Well… the cooling in our cluster room keeps the temperature at 18 degrees, but the CPU temperature can easily reach 60 degrees Celsius…
But what you probably refer to is the temperature at which binding experiments are performed. Now you should realise that there is no correlation typically between docking scores and binding affinity in general (read our related papers, e.g. Kastritis and Bonvin Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J. Proteome Research, 9, 2216-2225 (2010)).
And there are various algorithms used in docking. For example the first docking step in HADDOCK is performed by rigid body energy minimisation and there is simply no temperature defined in that. Probably time to do some more reading on the docking methodology.
But if i want to replicate this docking in my lab on a chip, then what temperature should i provide for the reaction? Temperature can easily impact reaction between aptamer and protein. Please help me out.
Please read carefully Alexandre’s answer. Depending on the stage of HADDOCK, the “temperature” typically varies from 0K to 2000K, if you want me to give you absurd, yet accurate, numbers.
Our modelling process is biased toward some local sampling, where we typically “freeze” the regions that are not interacting and only progressively introduce flexibility at the interface. Please read HADDOCK’s manual for more details, especially
the docking section (http://www.bonvinlab.org/software/haddock2.2/manual/).
As a final word, we cannot give you an answer if you expect a physical quantity that you can measure/set in the lab