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的含义。用标题“Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state” 的话，同时突出了方法和结果的含义。注意标题“Native proteins are surface-molten solids” 是结果的解释，而不是结果本身。用既广泛又具体的标题，这样才能吸引更多的读者。引言部分中心命题和标题都决定了以后，就该写引言了。第一件该做的事就是围绕中心命题来收集所有相关文献。搜索并研究所有最近和相关的文章(通过对中心命题关键字的搜索或用引用索引)。确认你有所有最新的论文。引用所有重要的文章。如果你不引用别人的文献，别人也不会引用你的！如果你想谁引用你的工作，你要先引用他的。你引用的文章越多，他们越可能阅读并引用你的文章。因为人们更加关注引用他们的论文。仔细读你所引用的文章，避免引用错误。在引用上，不要偷懒。引言的第一句最难写，因为它决定了你整个引言的走向。我的办法是把第一句和文章的标题连起来。在第一段以最基本和常见的术语来定义标题里用的一些术语。从这个术语，引入研究的领域和它的重要性。第二段应该对这个研究领域作一个鉴定性的论述。如果中心命题是关于解决一个问题的方法。这一段就应该指出这个当前研究中现存未解决的问题。描述解决这个问题的难度或挑战。第三段引入你提出的办法和它大致会带来什么效果。你可以大略地描述你的结果和它的含义。这里有个例子。 Assessing secondary structure assignments of protein structures by using pairwise sequence-alignment benchmarks, the secondary structure of a protein refers to the local conformation of its polypeptide backbone. Knowing secondary structures of proteins iessential for their structure classification, understanding folding dynamics and mechanis(s)ms, and discovering conserved structural/functional motifs. Secondary structure informatiis also useful for sequence and multiple sequence alignment, structure alignment,andsequ(on)ence to structure alignment (or threading). As a result, predicting secondary structures from protein sequences continues to be an active field of research fifty six years after Pauling and Corey first predicted that the most common regular patterns of proteibackbones are the α-helix and the β-sheet. Prediction and application of proteinsecon(n)dary structures rely on prior assignment of the secondary-structure elements from a given protein structure by human or computational methods. Many computational methods have been developed to automate the assignment of secondary structures. Examplare DSSP,STRIDE, DEFINE, P-SEA, KAKSI,P-CURVE, XTLSSTR,SECSTR,SEGNO,(es)and VoTAP. These methods are based on either the hydrogen-bond pattern, geometric features, expert knowledge or their combinations. However, they often disagree on their assignments. For example, disagreement among DSSP, P-CURVE, and DEFINE can be as large as 25%. More beta sheet is assigned by XTLSSTR and more pi-helix by SECSTR than by DSSP. The discrepancy among different methods is caused by non-ideal configurations of helices and sheets. As a result, defining the boundaries between helix, sheet, and coil is problematical and a significant source of discrepancies between different methods. Inconsistent assignment of secondary structures by different methods highlights the need for a criterion or a benchmark of “standard” assignments that could be used to assess and compare assignment methods. One possibility is to use the secondary structures assigned by the authors who solved the protein structures. STRIDE, in fact, has been optimized to achieve the highest agreement with the authors’ annotations. However, it is not clear what is the criterion used for manual or automatic assignment of secondary structures by different authors. Another possibility is to treat the consensus prediction by several methods as the gold standard. However, there is no obvious reason why each method should weight equally in assigning secondary structures and which method should be used in consensus. Other used criteriinclude helix-capping propensity, the deviation from ideal helical and sheet configurations,and(a)structural accuracy produced by sequence-to-structure alignment guided by secondary structure assignment. In th