Novel knowledge-based mean force potential at the profile level

Background: The development and testing of functions for the modeling of protein energetics is an important part of current research aimed at understanding protein structure and function. Knowledge-based mean force potentials are derived from statistical analyses of interacting groups in experimentally determined protein structures. Current knowledge-based mean force potentials are developed at the atom or amino acid level. The evolutionary information contained in the profiles is not investigated. Based on these observations, a class of novel knowledge-based mean force potentials at the profile level has been presented, which uses the evolutionary information of profiles for developing more powerful statistical potentials. Results: The frequency profiles are directly calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into binary profiles with a probability threshold. As a result, the protein sequences are represented as sequences of binary profiles ...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Qiwen Dong, Xiaolong Wang, Lei Lin
• Keywords: BMCBI 2006, Mean Force Potentials, Profile, Statistical Potentials