Platform for Physics-Based Methods in CASP (Comp. Rev. to LM007085)

说明(由申请人提供)：拟议补充工作的主要目标有三个(对LM-7085(P41)的补充： (1)提供检验和发展力场的持续机制。为了聚焦于力场问题，利益集团将确定并同意一种构象搜索方法。CASP 基础设施将用于提供测试机制。此外，还将收集、表征和提供各种不正确的(‘诱饵’)结构，以便进行基准测试。预测界将被要求贡献这些诱饵。作为CASP_D实验的一部分，已经建立了一个诱饵试验服务器。将向社区提供评估。进行个人基准测试的参与者也将被要求提供他们的测试结果。这样，就有可能客观地评估当前力场的优势和劣势，并确定改进它们的最有效方法。 (2)提供一个持续的机制来测试和发展构象搜索方法。许多小组已经发展出寻找构象空间以寻找功能构象的方法。一个主要的复杂因素是，大多数新的搜索也使用了新的力场，很难区分这两个组成部分的影响。为了专注于搜索问题，将在测试中使用一系列力场，一次一个。具体细节将由利益集团商定。CASP基础设施将用于提供测试机制。与潜在问题一样，将从预测社区寻找搜索问题的例子，并通过特定的搜索方法公开在这一集合上获得的结果。 (3)提供一个沟通系统，使项目成果能够在 以物理为基础的预测社区，参与指导该项目，并有效讨论结果的科学意义。如果没有社会的支持和信心，这些目标都不可能实现。我们认为，由于进行了CASP结构预测实验，我们处于有利地位，可以促进这种支持，但每一个组成部分都需要仔细协商。

DESCRIPTION (provided by applicant): The primary goals of the proposed supplementary effort are three-fold (supplement to LM-7085 (P41) : (1) To provide an ongoing mechanism to test and evolve force fields. To focus on the force field issues, a conformational search method will be identified and agreed upon by the interest group. The CASP infrastructure will be used to provide testing mechanism. In addition, a large variety of incorrect ('decoy') structures will be collected, characterized, and provided for benchmarking. The prediction community will be requested to contribute these decoys. A pilot server for decoys has already been set up as part of the CASP_D experiment. Evaluations will be made available to the community. Participants performing individual benchmarking will be asked to make available the results of their tests as well. In this way, it will be possible to objectively assess the strengths and weaknesses of present force fields, and to identify the most effective ways of improving them. (2) To provide an ongoing mechanism to test and evolve conformational search methods. Many groups have developed methods of searching the conformational space for the functional conformation. A major complicating factor is that most new searches also use new force fields, and it has been difficult to separate the effects of the two components. To focus on the search issues, a series of force fields will be used in testing, one at a time. Details will be agreed upon by the interest group. The CASP infrastructure will be used to provide testing mechanism. As with potentials, examples of search problems will be sought from the prediction community, and the results obtained on this collection with particular search methods made public. (3) To provide a communication system that will allow full sharing of the results of the project within the physics-based prediction community, participation in directing the project, and effective discussion of the scientific significance of the results. None of the objectives can be achieved unless they have the support and confidence of the community. We believe that we are well placed to foster such support as a result of the CASP structure prediction experiment, but each component will require careful consultation.