The eternal debate – one score function to rule them all?
~ contributed by Julia Koehler Leman Molecular modeling packages use various types of score functions, depending on the task and their required atomistic level descriptions. For instance, molecular dynamics simulation packages often use a molecular mechanics force field to model small molecules, peptides and small proteins, and allow exploring the folding trajectory of the latter two. The modeling of chemical reactions requires a description of the electron configurations through quantum-mechanical force fields, which are expensive to compute and only possible for small systems. A combined QM/MM (quantum mechanics / molecular mechanics) approach allows modeling chemical reactions in larger systems such as enzymes. Monte-Carlo simulation packages often rely (at least partly) on knowledge-based score functions that are statistically derived from experimentally validated datasets through an inverse Boltzmann relationship (see Figure). Figure: Most prevalent ...