{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T20:27:19Z","timestamp":1778876839261,"version":"3.51.4"},"reference-count":59,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Recently, we made synthetic proteins from non-coding DNA of Escherichia coli . Encouraged by this, we asked: can we artificially express pseudogenes into novel and functional proteins? What kind of structures would be generated? Would these proteins be stable? How would the organism respond to the artificial reactivation of pseudogenes?<\/jats:p><jats:p>Results: To answer these questions, we studied 16 full-length protein equivalents of pseudogenes. The sequence-based predictions indicated interesting molecular and cellular functional roles for pseudogene-derived proteins. Most of the proteins were predicted to be involved in the amino acid biosynthesis, energy metabolism, purines and pyrimidine biosynthesis, central intermediary metabolism, transport and binding. Interestingly, many of the pseudogene-derived proteins were predicted to be enzymes. Furthermore, proteins showed strong evidence of stable tertiary structures. The prediction scores for structure, function and stability were found to be favorable in most of the cases.<\/jats:p><jats:p>Impact: To our best knowledge, this is the first such report that predicts the possibility of making functional and stable proteins from pseudogenes. In future, it would be interesting to experimentally synthesize and validate these predictions.<\/jats:p><jats:p>Contact: \u00a0pawan.dhar@snu.edu.in<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu615","type":"journal-article","created":{"date-parts":[[2014,9,19]],"date-time":"2014-09-19T04:50:41Z","timestamp":1411102241000},"page":"33-39","source":"Crossref","is-referenced-by-count":16,"title":["Making novel proteins from pseudogenes"],"prefix":"10.1093","volume":"31","author":[{"given":"P. R.","family":"Shidhi","sequence":"first","affiliation":[{"name":"1 Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, 2 Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, 3 Bioclues.org, India, 4 Bioclues.org, Denmark, 5 National College, University of Kerala, Trivandrum- 695 009, 6 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and 7 Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Prashanth","family":"Suravajhala","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, 2 Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, 3 Bioclues.org, India, 4 Bioclues.org, Denmark, 5 National College, University of Kerala, Trivandrum- 695 009, 6 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and 7 Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India"},{"name":"1 Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, 2 Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, 3 Bioclues.org, India, 4 Bioclues.org, Denmark, 5 National College, University of Kerala, Trivandrum- 695 009, 6 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and 7 Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India"},{"name":"1 Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, 2 Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, 3 Bioclues.org, India, 4 Bioclues.org, Denmark, 5 National College, University of Kerala, Trivandrum- 695 009, 6 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and 7 Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aysha","family":"Nayeema","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, 2 Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, 3 Bioclues.org, India, 4 Bioclues.org, Denmark, 5 National College, University of Kerala, Trivandrum- 695 009, 6 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and 7 Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Achuthsankar S.","family":"Nair","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, 2 Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, 3 Bioclues.org, India, 4 Bioclues.org, Denmark, 5 National College, University of Kerala, Trivandrum- 695 009, 6 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and 7 Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shailja","family":"Singh","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, 2 Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, 3 Bioclues.org, India, 4 Bioclues.org, Denmark, 5 National College, University of Kerala, Trivandrum- 695 009, 6 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and 7 Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pawan K.","family":"Dhar","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum- 695 581, India, 2 Bioinformatics.Org, 28 Pope Street, Hudson, MA 01749, USA, 3 Bioclues.org, India, 4 Bioclues.org, Denmark, 5 National College, University of Kerala, Trivandrum- 695 009, 6 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh- 201 314, and 7 Centre for Systems and Synthetic Biology, University of Kerala, Kariyavattom, Trivandrum- 695 581, 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