Hello everybody- > Molecular models are the result of numbers emerging from computer programs. > The results of such computations do not reflect anything in nature. There's > no experimental evidence whatsoever, making modelling a very theoretical -- > in my eyes uninteresting -- exercise.
Molecular dynamics is starting to incorporate experimental evidence into molecular dynamics simulations, e.g. from EM Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, Klaus Schulten Structure. 2008 May; 16(5): 673–683. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430731/?tool=pubmed (This stills needs an X-ray structure as starting point). We are already frequently confronted in EM with deciding how much of a fitted structure is modeling and how much is supported by evidence. At some point it is a matter of degree, not principle. (This point is where you can see mostly blobs). By the way, molecular dynamics, which is based on first principles, is quite different from (homology) modeling in bioinformatics. The latter is indeed merely a very educated guess that often works. Oh, and the last paragraph of the paper is interesting... -Christoph -- | Dr Christoph Best <b...@ebi.ac.uk> http://www.ebi.ac.uk/~best | Project Leader Electron Microscopy Data Bank, PDB Europe | European Bioinformatics Institute, Cambridge, UK +44-1223-492649
