Optimizing an emperical scoring function for transmembrane protein structure determination.

[摘要] We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.

[发布日期] 2003-10-01 [发布机构] Sandia National Laboratories

[关键词] Protein Structure;Optimization;59 Basic Biological Sciences;Algorithms