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is paper, we propose to use sequence-alignment benchmarks for assessing secondary structure assignments. These benchmarks are produced by 3D-structure alignment of structurally homologous proteins. Instead of assessing the accuracy of secondary-structure assignment directly, which is not yet feasible, we compare the two assignments of secondary structures in structurally aligned positions. We assume that the best method should assign the same secondary-structure element to the highest fraction of structurally aligned positions. Certainly, structurally aligned positions do not always have the same secondary structures. Moreover, different structure-alignment methods do not always produce the same lt. Nevertheless, this criterion provides a means to locate a secondary-structure assig(resu)nment method that is most consistent with tertiary structure alignment. We suggest that this approach provides an objective evaluation of secondary structure assignment methods. 在这个例子里，标题推荐了一个评估指派蛋白质二级结构的方法。第一段以二级结构的定义开始（与标题相连)。整段描述了二级结构的重要性。最后一句过渡到指派二级结构的计算方法（下一段的主题)。注意“计算方法”放在句子的最后是为了强调而且和第二段的开始连接在起来。第二段则聚焦在计算方法中存在的问题。旧信息“计算方法”逐渐的变到了“它们的不一致”。第三段的第一句把主题从“不一致”（旧信息）转变成了“评估的办法”（新信息)。然后，介绍了这个领域已有的工作。第四段引入新方法并讨论了新方法的优点。第五段（这里没有给出）将会简要地讨论结果。每一个引言应该包括研究领域的介绍和意义，做这工作的具体原因，结果和隐含的意义。一般而言，读者读完引言，对论文的来龙去脉就应该清清楚楚了。讨论部分现在到了你写论文的最后一部分。很多人认为讨论部分最难写。他们常常不知道该写什么。学生常常不能把结果从他们的解释、含意和结论中分离出来。此外，他们不善于思考可能存在的其他解释。好的讨论通常以得到的结果和解释的评论开始。其它可用于讨论的内容有：参数改变对结果的影响，与其他研究相比还有待解决的问题，将来或正在进行的工作（防止别人从事你显而易见的，立刻就能实现的后续工作)。这里有一段文章中的讨论部分。 One question about the complex homopolymer phase diagram presented here is whether it is caused by the discontinuous feature of the square-well potential. We cannot give a direct answer because the DMD silation is required to obtain well-converged results for the thermodynamics. However, the critical ph(mu)enomena predicted for a fluid composed of partiles interacting with a square-well potentil are as realistic as those predicted for a fluidco(c)mposed of particles interacting withaLJp(a)otential. Also an analogous complex phase diagram is found in simulations of LJ clusters. The present results for square-well homopolymers may well be found in more realistic homopolymer models and even in real polymers. 这一段探究了可供选择的解释。摘要部分整篇文章写完了。你需要写文章的摘要了。典型的摘要包括课题领域的重要性（回到标题)，要研究的问题，你方法的独特性，结果的意义和影响。这里有个例子。 How to make an objective assignment of secondary structures based on a protein structure is an unsolved problem. Defining the boundaries between helix, sheet, and coil structures is arbitrary, and commonly accepted standard assignments do not exist. Here, we propose a criterion that assesses secondary-structure assignment based on the similarity of the secondary structures assigned to structurally aligned residues in sequence-alignment benchmarks. Thiiteriiused to rank six secondary-structure assignmentmethods: STRIDE, DSSP, SECSTR,(scr) KAKSI (on),(s) P-SEA, and SEGNO with three established sequence-alignment benchmarks (PREFAB, SABmark and SALIGN). STRIDE and KAKSI achieve comparable success rates in assigning the same secondary structure elements to structurally aligned residues in the three benchmarks. Their success rates are between 1-4% higher than those of the other four methods. The consensus of STRIDE, KAKSI, SECSTR, and P-SEA, called SKSP, improves assignments over the best single method in each benchmark by an additional 1%. These results support the usefulness of the sequence alignment benchmarks as the benchmarks for secondary structure ass