Comparative estimation of vibrational entropy changes in proteins through normal modes analysis

We compare the vibrational entropy changes of proteins calculated using a full and a number of approximate normal modes analysis methods. The vibrational entropy differences for three conformational changes and three protein binding interactions were computed. In general, the approximate methods yield good estimates of the vibrational entropy change in a fraction of the time required by full normal modes analysis. The absolute entropies are either overestimated or greatly underestimated, but the difference is sufficiently accurate for some methods. This indicates that some of the approximate methods can give reasonable estimates of the associated vibrational entropy changes, making them suitable for inclusion in free energy calculations. (C) 2004 Elsevier Inc. All rights reserved.