Protein folding using fragment assembly and physical energy function

摘要

We perform a systematic study of the effects of sequence-independent backbone interactions and sequence-dependent side-chain interactions on protein folding using fragment assembly and physical energy function.Structures for ten proteins belonging to various structural classes are predicted only with Lennard-Jones interaction between backbone atoms.We find nativelike structures for beta proteins,suggesting that for proteins in this class,the global tertiary structures can be determined mainly by sequence-independent backbone interactions.On the other hand,for alpha proteins,nonlocal hydrophobic side-chain interaction is also required to obtain nativelike structures.