Background#R##N#Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the Ab Initio energy function can be used to improve threading, especially for the weakly/distant homologous templates.
['Mingfu Shao', 'Sheng Wang', 'Chao Wang', 'Xiongying Yuan', 'Shuai Cheng Li', 'Wei-Mou Zheng', 'Dongbo Bu']
Incorporating Ab Initio energy into threading approaches for protein structure prediction