Protein movement can be simulated three times as fast than had been thought possible up to now. Researchers from Groningen achieved the gain in speed by leaving out the calculations concerning hydrogen atoms. Meanwhile research groups around the world are adapting their simulation programs.
Up until now researchers calculated all of the positions of atoms in a protein molecule after two femtoseconds. A femtosecond is one millionth of a billionth of a second. The research from Groningen reveals that steps of 7 femtoseconds are also good enough. With this the simulation is three times as fast. A number of research groups are already using the results from the Groningen study.
Steps of 7 femtseconds ignore the forces which occur between hydrogen atoms. The researchers have demonstrated that these forces are not relevant for the simulation. Indeed, taking into account how the forces were always described up until now, they are best left out of the calculations.
Michel Philippens | alfa
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