Computational protein design is a challenge for implicit solvation models.

ABSTRACT: Increasingly complex schemes for representing solvent effects in an implicit fashion are being used in computational analyses of biological macromolecules. These schemes speed up the calculations by orders of magnitude and are assumed to compromise little on essential features of the solvation phenomenon. In this work we examine this assumption. Five implicit solvation models, a surface area-based empirical model, two models that approximate the generalized Born treatment and a finite difference Poisson-Boltzmann method are challenged in situations differing from those where these models were calibrated. These situations are encountered in automatic protein design procedures, whose job is to select sequences, which stabilize a given protein 3D structure, from a large number of alternatives

SUBMITTER: Jaramillo A 

PROVIDER: S-EPMC1304995 | biostudies-literature | 2005 Jan

REPOSITORIES: biostudies-literature