Folding Forum

My son is a cell and molecular biologist working in an HIV & cancer research lab at a medical school in Virginia. He asked me whether you were using a retrospective approach (reverse extrapolating known proteins to the linear sequence using x-ray crystallography) or free energy algorithms mapping a protein from scratch.
I'm an English teacher, so of course I had no answer.
Can you answer this question for me for him?
Cheers

I suggest you point him to our papers page and he can see all the technical details there.

http://folding.stanford.edu/English/Science

http://folding.stanford.edu/English/Papers

http://folding.stanford.edu/English/Awards

abuyonus wrote:He asked me whether you were using a retrospective approach (reverse extrapolating known proteins to the linear sequence using x-ray crystallography) or free energy algorithms mapping a protein from scratch.

Neither -- we're doing molecular dynamics simulations, which is essentially solving Newton's laws for the motions of all the atoms of the protein (and the solvent). Of course to do this you need forces, of which there are several types (bond-stretching, electrostatic forces, etc.) which are given relative strengths to make them comparable to the forces in quantum mechanics calculations, or to the energies observed in experiments.

Feel free to ask for clarification of that jumble.

Dan

I think it depends on what is meant by "free energy here". THat's why I suggested your son just look at our papers. People use different names, simplified jargon, etc, and it's best to just see exactly what we're doing rather than use words which might mean one thing to one person, but another to another.