Constraint Logic Programming approach to protein structure prediction -: art. no. 186
Constraint Logic Programming approach to protein structure prediction -: art. no. 186
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DOI：
10.1186/1471-2105-5-186
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发表时间：
2004-11-30
影响因子：
3
通讯作者：
Fogolari, F
中科院分区：
文献类型：
--
作者：
Dal Pal첫, A;Dovier, A;Fogolari, F
背景：蛋白质结构预测问题是生物科学中最具挑战性的问题之一。已经提出了许多使用数据库信息和/或简化的蛋白质模型的方法。蛋白质结构预测问题可以用最优化问题的形式来表示。约束逻辑编程是一种适用于解决组合优化问题的陈述性编程范式，尽管它很重要，但很少有人用它来解决这个问题。结果：约束逻辑编程技术被应用于人脸中心立方格模型上的蛋白质结构预测问题。被赋予约束概念的分子动力学技术也被开发出来。即使使用一个非常简化的模型，在面心立方晶格模型上的约束逻辑编程也允许我们对一些小蛋白质获得可接受的结果。作为测试实现，它们的(已知的)二级结构和二硫键的存在被用作约束。用这种方法得到的简化结构被转换成具有合理结构的所有原子模型。结论：对小分子蛋白质的研究结果表明，约束逻辑编程技术可以用于蛋白质简化模型的研究，可以将其转化为真实的全原子模型。约束逻辑编程相对于其他更多探索的方法的优势在于快速的软件原型设计，在编码启发式的简单方式，以及在该研究领域中所取得的所有进展的利用，例如在约束传播及其用于修剪巨大的搜索空间。
Background: The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems.Results: Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known) secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a well-established technique as molecular dynamics.Conclusions: The results obtained on small proteins show that Constraint Logic Programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The advantage of Constraint Logic Programming over other, much more explored, methodologies, resides in the rapid software prototyping, in the easy way of encoding heuristics, and in exploiting all the advances made in this research area, e.g. in constraint propagation and its use for pruning the huge search space.