Link to full page (citation export, more details):

Predicting free energy changes using structural ensembles

Full Text PDF:

PDF icon nature09.pdf


PDF icon nature09_s.pdf

A. Benedix; C.M. Becker; B.L. de Groot; A. Caflisch; R.A. Böckmann

Journal: Nat. Methods
Year: 2009
Volume: 6
Issue: 1
Pages: 3-4
DOI: 10.1038/nmeth0109-3
Type of Publication: Journal Article

Mutation; Protein Binding; Protein Folding; Proteins; Thermodynamics


Reliable and fast computation of protein free energy is crucial for protein-structure analysis, structure-based protein design and protein docking. Rigorous treatments based on physical effective energy functions involve computationally expensive methods such as free energy perturbation, which are time–consuming and are thus incompatible with the need to perform extensive scans. Commonly used fast methods, in turn, involve empirically derived scoring functions and usually do not include protein flexibility or are based on statistical potentials and are therefore highly dependent on the availability of case-dependent experimental training data. Hence, such methods are inherently limited in accuracy and applicability.

(In lieu of a true abstract, this is the first paragraph.)