Quod erat demonstrandum The mystery of experimental validation of apparently erroneous computational analyses of protein sequences 英文参考文献.docVIP

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Quod erat demonstrandum The mystery of experimental validation of apparently erroneous computational analyses of protein sequences 英文参考文献.doc

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Quod erat demonstrandum The mystery of experimental validation of apparently erroneous computational analyses of protein sequences 英文参考文献

/2001/2/12/research/0051.1 Research Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences Lakshminarayan M Iyer*, L Aravind*, Peer Bork?, Kay Hofmann?, Arcady R Mushegian§, Igor B Zhulin? and Eugene V Koonin* Addresses: *National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. ?EMBL, Biocomputing, Meyerhofstrasse 1, 69117 Heidelberg, Germany. ?MEMOREC Stoffel GmbH, K?ln D-50829, Germany. §Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64410, USA. ?School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA. *Correspondence: Eugene V Koonin. E-mail: koonin@ Published: 13 November 2001 Received: 3 July 2001 Revised: 7 September 2001 Accepted: 4 October 2001 Genome Biology 2001, 2(12):research0051.1–0051.11 The electronic version of this article is the complete one and can be found online at /2001/2/12/research/0051 ? 2001 Iyer et al., licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: Computational predictions are critical for directing the experimental study of protein functions. Therefore it is paradoxical when an apparently erroneous computational prediction seems to be supported by experiment. Results: We analyzed six cases where application of novel or conventional computational methods for protein sequence and structure analysis led to non-trivial predictions that were subsequently supported by direct experiments. We show that, on all six occasions, the original prediction was unjustified, and in at least three cases, an alternative, well-supported computational prediction, incompatible with the original one, could be derived. The most unusual cases involved the identification of an archaeal cysteinyl-tRNA synthetase, a dihydropteroate synthase and