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Revisiting the prediction of protein function at CASP6

机译：重新审视CASP6蛋白质功能的预测

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The ability to predict the function of a protein, given its sequence and/or 3D structure, is an essential requirement for exploiting the wealth of data made available by genomics and structural genomics projects and is therefore raising increasing interest in the computational biology community. To foster developments in the area as well as to establish the state of the art of present methods, a function prediction category was tentatively introduced in the 6th edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP) worldwide experiment. The assessment of the performance of the methods was made difficult by at least two factors: (a) the experimentally determined function of the targets was not available at the time of assessment; (b) the experiment is run blindly, preventing verification of whether the convergence of different predictions towards the same functional annotation was due to the similarity of the methods or to a genuine signal detectable by different methodologies. In this work, we collected information about the methods used by the various predictors and revisited the results of the experiment by verifying how often and in which cases a convergent prediction was obtained by methods based on different rationale. We propose a method for classifying the type and redundancy of the methods. We also analyzed the cases in which a function for the target protein has become available. Our results show that predictions derived from a consensus of different methods can reach an accuracy as high as 80%. It follows that some of the predictions submitted to CASP6, once reanalyzed taking into account the type of converging methods, can provide very useful information to researchers interested in the function of the target proteins.
机译：给定蛋白质的序列和/或3D结构，预测蛋白质功能的能力是利用基因组学和结构基因组学计划提供的大量数据的基本要求，因此引起了对计算生物学界的越来越多的关注。为了促进该领域的发展并建立当前方法的先进水平，在第六版《蛋白质结构预测技术的关键评估技术》（CASP）全球实验中，暂时引入了功能预测类别。至少有两个因素使评估方法的性能变得困难：（a）在评估时无法通过实验确定目标的功能; （b）实验是盲目进行的，无法验证对相同功能注释的不同预测的收敛是由于方法的相似性还是由于不同方法可检测到的真实信号。在这项工作中，我们收集了有关各种预测器使用的方法的信息，并通过验证通过基于不同原理的方法获得收敛预测的频率和次数来重新审视实验结果。我们提出了一种对方法的类型和冗余进行分类的方法。我们还分析了目标蛋白功能已可用的情况。我们的结果表明，从不同方法的共识得出的预测可以达到高达80％的准确性。因此，考虑到收敛方法的类型，重新分析提交给CASP6的某些预测，可以为对靶蛋白功能感兴趣的研究人员提供非常有用的信息。

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