Predicting active site residue annotations in the Pfam database.
Predicting active site residue annotations in the Pfam database.
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DOI：
10.1186/1471-2105-8-298
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发表时间：
2007-08-09
影响因子：
3
通讯作者：
Finn RD
中科院分区：
文献类型：
--
作者：
Mistry J;Bateman A;Finn RD
大约5%的Pfam家族是具有酶活性的，但在这些家族中只有一小部分序列（<0.5%）其负责催化的残基已被确定。为了增加Pfam数据库中活性位点的注释，我们制定了一套严格的规则，旨在降低假阳性率，从而能够将实验确定的活性位点残基数据转移到同一Pfam家族的其他序列中。
我们创建了一个庞大的预测活性位点残基数据库。在将我们的活性位点预测结果与UniProtKB、催化位点图谱（Catalytic Site Atlas）、PROSITE和MEROPS中的结果进行比较时，我们发现我们做出了许多新的预测。在对这些数据库做出而我们未做出的一小部分预测进行研究时，我们发现这些序列不符合我们严格的预测标准。我们评估了我们方法的敏感性和特异性，并估计我们预测的序列中只有3%是假阳性。
我们已经预测了606110个活性位点残基，其中94%在UniProtKB中未被发现，并且使Pfam中的活性位点注释增加了200多倍。尽管是为Pfam实施的，但我们开发的用于转移数据的工具可应用于任何具有相关实验活性位点数据的比对，并且可供下载。我们的活性位点预测在每次Pfam发布时都会重新计算，以确保它们全面且最新。它们提供了现有的最大的活性位点注释数据库之一。
Approximately 5% of Pfam families are enzymatic, but only a small fraction of the sequences within these families (<0.5%) have had the residues responsible for catalysis determined. To increase the active site annotations in the Pfam database, we have developed a strict set of rules, chosen to reduce the rate of false positives, which enable the transfer of experimentally determined active site residue data to other sequences within the same Pfam family. We have created a large database of predicted active site residues. On comparing our active site predictions to those found in UniProtKB, Catalytic Site Atlas, PROSITE and MEROPS we find that we make many novel predictions. On investigating the small subset of predictions made by these databases that are not predicted by us, we found these sequences did not meet our strict criteria for prediction. We assessed the sensitivity and specificity of our methodology and estimate that only 3% of our predicted sequences are false positives. We have predicted 606110 active site residues, of which 94% are not found in UniProtKB, and have increased the active site annotations in Pfam by more than 200 fold. Although implemented for Pfam, the tool we have developed for transferring the data can be applied to any alignment with associated experimental active site data and is available for download. Our active site predictions are re-calculated at each Pfam release to ensure they are comprehensive and up to date. They provide one of the largest available databases of active site annotation.
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Merops：肽酶数据库。
影响因子：
14.9
作者：
Rawlings, Neil D.;Morton, Fraser R.;Barrett, Alan J.
通讯作者：
Barrett, Alan J.
影响因子：
3
作者：
Mistry J;Bateman A;Finn RD
通讯作者：
Finn RD
Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
14.9
作者：
Mulder NJ;Apweiler R;Attwood TK;Bairoch A;Bateman A;Binns D;Bork P;Buillard V;Cerutti L;Copley R;Courcelle E;Das U;Daugherty L;Dibley M;Finn R;Fleischmann W;Gough J;Haft D;Hulo N;Hunter S;Kahn D;Kanapin A;Kejariwal A;Labarga A;Langendijk-Genevaux PS;Lonsdale D;Lopez R;Letunic I;Madera M;Maslen J;McAnulla C;McDowall J;Mistry J;Mitchell A;Nikolskaya AN;Orchard S;Orengo C;Petryszak R;Selengut JD;Sigrist CJ;Thomas PD;Valentin F;Wilson D;Wu CH;Yeats C
通讯作者：
Yeats C
影响因子：
5.6
作者：
Greaves, R;Warwicker, J
通讯作者：
Warwicker, J