Folding patterns in protein sequences
Corpas, M. 2007. Folding patterns in protein sequences. PhD thesis University of Manchester https://doi.org/10.6084/m9.figshare.964811.v1
Corpas, M. 2007. Folding patterns in protein sequences. PhD thesis University of Manchester https://doi.org/10.6084/m9.figshare.964811.v1
| Title | Folding patterns in protein sequences |
|---|---|
| Type | PhD thesis |
| Authors | Corpas, M. |
| Abstract | In the wake of numerous fruitful genome projects, a growing number of protein sequences remain uncharacterised. Generally, computational techniques have not been developed to distinguish between regions that are conserved in proteins owing to evolutionary pressures to maintain structure and those that are conserved in order to preserve function. Interestingly, there is experimental evidence to suggest that some residues are conserved to maintain the protein fold, while others are conserved to maintain function at the cost of structural stability. Combining this observation with a fingerprint analysis of a representative dataset of globular proteins, here we explore folding signals affecting sequence conservation and, in particular, motifs. Initially, we aimed at determining whether folding signals are encoded in sequence motifs. It was found that those regions best conserved in evolutionary time (i.e., superfamily motifs) tend to concentrate most favourable folding signals. A folding score, combining folding signals affecting sequence conservation, was created to distinguish structurally favourable motifs from those that are not. We found that integration of folding signals indeed added value over individual ones. Folding score troughs were observed to be highly conserved, while peaks had variable degrees of conservation. Coupled with the degree of conservation of residues, the folding score was used to delineate regions that are likely to contribute to (i) the stability of the fold (structural motifs), and (ii) the function of the protein (functional motifs). We have presented a few simple case-studies to illustrate how the combined data can be used to pinpoint motifs with potential structural and functional roles. This method offered a means of automatic motif detection, which could be used for protein family characterisation and functional/structural annotation of evolutionarily conserved regions. As folding information is contained in superfamily motifs, we explored whether folding signals can be used to enhance the diagnostic performance of distant similarity search. For that purpose, fingerprints were created according to motif boundaries imposed by the folding score. Automatically created motifs provided a new means to guide motif selection in fingerprints, where manually selected motifs had been chosen in an ad hoc manner, owing to being extracted from a highly conserved alignment. Similarly, fingerprinting using only automatically defined structural motifs, had a greater number of distant matches than manually created fingerprints. Thus, this new approach to fingerprinting offers a complementary method to manual fingerprint creation and the ability to characterise conserved protein regions from a structural point of view. |
| Year | 2007 |
| Publication dates | |
| Published | 2007 |
| Digital Object Identifier (DOI) | https://doi.org/10.6084/m9.figshare.964811.v1 |
Trends in suicidal behavior among hospitalized adolescents in Spain over two decades.
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Generalisation of genomic findings and applications of polygenic risk scores
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Is SARS- CoV-2 the only cause of long-COVID?
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Implementation of individualised polygenic risk score analysis: a test case of a family of four
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Transferability of genetic risk scores in African populations
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Editorial: Personal Genomes: Accessing, Sharing, and Interpretation
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Whole Genome Interpretation for a Family of Five
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Simplifying access to human genomic data: community platform Repositive.io
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Phenotype-loci associations in networks of patients with rare disorders: application to assist in the diagnosis of novel clinical cases
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A FAIR guide for data providers to maximise sharing of human genomic data
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Personal Genome Project UK (PGP-UK): A research and citizen science hybrid project in support of personalized medicine
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APPLaUD: Access for patients and participants to individual level uninterpreted genomic data
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Four simple recommendations to encourage best practices in research software [version 1; referees: awaiting peer review]
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Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination.
Corpas, M. 2017. Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC Biology. 15 86. https://doi.org/10.1186/s12915-017-0419-x
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Systematic identification of phenotypically enriched loci using a patient network of genomic disorders
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Progress on the genome characterisation of D. alata
Corpas, M. 2016. Progress on the genome characterisation of D. alata. Plant and Animal Genome XXIV Conference. Town & Country Resort & Convention Center 09 - 13 Jan 2016
Cutting Edge: Lessons from fraxinus, a crowd-sourced citizen science game in genomics
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GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
Atwood, T.K., Bongcam-Rudloff, E., Brazas, M.E., Corpas, M., Gaudet, P., Lewitter, F., Mulder, N., Palagi, P.M., Schneider, M.V., van Gelder, C.W.G., Attwood, T.K., Banag, C., Blackford, S., Blatter, M.C., Bongcam-Rudloff, E., Brazas, M.D., Brooksbank, C., Budd, A., Charleston, M., Christoffels, A., Conesa, A., Crowe, M., Davies, A., de Crecy-Lagard, V., De Las Rivas, J., Doyle, M., Edwards, R., Facchiano, A., Fernandes, P., Gaeta, B., Gaudet, P., Heger, A., Herringa, J., Hughes, D., Jimenez, R.C., Kille, P., Korpelainen, E., Kumuthini, J., Lewitter, F., MacLean, D., Martinez, S.A.R., McGrath, A., Michalopoulos, I., Mulder, N., Ouellette, B.F., Palagi, P.M., Pearson, W.R., Qi, W., Romano, P., Rother, K., Sansone, S-A., Schneider, M.V., Schönbach, C., Tastan-Bishop, O., Trelles, O., Twells, R., van Gelder, C.W.G., Via, A., Vriend, G., Warnow, T., Watson, M., Westervelt, N. and Zanzoni, A. 2015. GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training. PLOS Computational Biology. 11 (5) e1004281. https://doi.org/10.1371/journal.pcbi.1004143
Crowdsourced direct-to-consumer genomic analysis of a family quartet
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The GOBLET training portal: A global repository of bioinformatics training materials, courses and trainers
Corpas, M., Jimenez, R.C., Bongcam-Rudloff, E., Budd, A., Brazas, M.D., Fernandes, P.L., Gaeta, B., Van Gelder, C., Korpelainen, E., Lewitter, F., McGrath, A., MacLean, D., Palagi, P.M., Rother, K., Taylor, J., Via, A., Watson, M., Schneider, M.V. and Attwood, T.K. 2015. The GOBLET training portal: A global repository of bioinformatics training materials, courses and trainers. Bioinformatics. 31 (1), pp. 140-142. https://doi.org/10.1093/bioinformatics/btu601
Ten Simple Rules for Organizing an Unconference
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Future opportunities and trends for e-infrastructures and life sciences: Going beyond the grid to enable life science data analysis
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A quick guide for building a successful bioinformatics community
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DNAContentViewer a BioJS component to visualise GC/AT Content
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wigExplorer, a BioJS component to visualise wig data
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BioJS: An open source standard for biological visualisation - its status in 2014
Corpas, M., Jimenez, R., Carbon, S.J., GarcÍa, A., Garcia, L., Goldberg, T., Gomez, J., Kalderimis, A., Lewis, S.E., Mulvany, I., Pawlik, A., Rowland, F., Salazar, G., Schreiber, F., Sillitoe, I., Spooner, W.H., Thanki, A.S., Villaveces, J.M., Yachdav, G. and Hermjakob, H. 2014. BioJS: An open source standard for biological visualisation - its status in 2014. F1000Research. 3 55. https://doi.org/10.12688/f1000research.3-55.v1
The BioJS article collection of open source components for biological data visualisation.
Corpas, M. 2014. The BioJS article collection of open source components for biological data visualisation. F1000Research. 3 56. https://doi.org/10.12688/f1000research.3-56.v1
The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013
de Ridder, J., Bromberg, Y., Michaut, M., Satagopam, V.P., Corpas, M., Macintyre, G. and Alexandrov, T. 2013. The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1003350
Bioinformatics workflows and web services in systems biology made easy for experimentalists
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BioJS: an open source JavaScript framework for biological data visualization
Gómez, J., García, L.J., Salazar, G.A., Villaveces, J., Gore, S., García, A., Martín, M.J., Launay, G., Alcántara, R., Del-Toro, N., Dumousseau, M., Orchard, S., Velankar, S., Hermjakob, H., Zong, C., Ping, P., Corpas, M. and Jiménez, R.C. 2013. BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics. 29 (8), pp. 1103-1104. https://doi.org/10.1093/bioinformatics/btt100
iAnn: an event sharing platform for the life sciences
Jimenez, R.C., Albar, J.P., Bhak, J., Blatter, M.C., Blicher, T., Brazas, M.D., Brooksbank, C., Budd, A., De Las Rivas, J., Dreyer, J., van Driel, M.A., Dunn, M.J., Fernandes, P.L., van Gelder, C.W., Hermjakob, H., Ioannidis, V., Judge, D.P., Kahlem, P., Korpelainen, E., Kraus, H.J., Loveland, J., Mayer, C., McDowall, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Salazar, G.A., Schneider, R., Via, A., Villaveces, J.M., Yu, P., Schneider, M.V., Attwood, T.K. and Corpas, M. 2013. iAnn: an event sharing platform for the life sciences. Bioinformatics. 29 (15), pp. 1919-1921. https://doi.org/10.1093/bioinformatics/btt306
Crowdsourcing the corpasome
Corpas M 2013. Crowdsourcing the corpasome. Source Code for Biology and Medicine. 8 13. https://doi.org/10.1186/1751-0473-8-13
A genome blogger manifesto
Corpas, M. 2012. A genome blogger manifesto. GigaScience. 1 (1) 15. https://doi.org/10.1186/2047-217x-1-15
A family experience of personal genomics
Corpas, M. 2012. A family experience of personal genomics. Journal of Genetic Counseling. 21 (3), pp. 386-391. https://doi.org/10.1007/s10897-011-9473-7
How not to be a bioinformatician
Corpas, M., Fatumo, S. and Schneider, R. 2012. How not to be a bioinformatician. Source Code for Biology and Medicine. 7 3. https://doi.org/10.1186/1751-0473-7-3
DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders.
Swaminathan, G.J., Bragin, E., Chatzimichali, E.A., Corpas, M., Bevan, A.P., Wright, C.F., Carter, N.P., Hurles, M.E. and Firth, H.V. 2012. DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. Human Molecular Genetics. 21 (R1), pp. R37-R44. https://doi.org/10.1093/hmg/dds362
Interpretation of genomic copy number variants using DECIPHER
Corpas, M., Bragin, E., Clayton, S., Bevan, P. and Firth, H.V. 2012. Interpretation of genomic copy number variants using DECIPHER. Current Protocols in Human Genetics. Chapter 8:Unit 8.14. https://doi.org/10.1002/0471142905.hg0814s72
Spanish cuts: more economic damage.
Corpas, M. 2012. Spanish cuts: more economic damage. Nature. 487 38. https://doi.org/10.1038/487038d
Bamako 2009 Conference on the Bioinformatics of Infectious Diseases
Corpas, M., Doumbia, S., Gascuel, O. and Mulder, N. 2011. Bamako 2009 Conference on the Bioinformatics of Infectious Diseases. Infection, Genetics and Evolution. 11 (4), pp. 695-697. https://doi.org/10.1016/j.meegid.2011.02.012
myKaryoView: a light-weight client for visualization of genomic data
Jimenez, R.C., Salazar, G.A., Gel, B., Dopazo, J., Mulder, N. and Corpas, M. 2011. myKaryoView: a light-weight client for visualization of genomic data. PLoS ONE. 6 (10) e26345. https://doi.org/10.1371/journal.pone.0026345
DECIPHER: Shedding Light on Chromosomal Imbalance and Phenotype Interpretation
Corpas, M., Richards, S., Bevan, P., van Vooren, S., Pettett, R., Firth, H. and Carter, N. 2009. DECIPHER: Shedding Light on Chromosomal Imbalance and Phenotype Interpretation. 7th European Cytogenetics Conference. Stockholm, Sweden 04 - 07 Jul 2009
DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.
Firth, H.V., Richards, S.M., Bevan, A.P., Clayton, S., Corpas, M., Rajan, D., Van Vooren, S., Moreau, Y., Pettett, R.M. and Carter, N.P. 2009. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. The American Journal of Human Genetics. 84 (4), pp. P524-533. https://doi.org/10.1016/j.ajhg.2009.03.010
ENFIN - An integrative structure for systems biology
Reisinger, F., Corpas, M., Hancock, J., Hermjakob, H., Birney, E. and Kahlem, P. 2008. ENFIN - An integrative structure for systems biology. in: International Workshop on Data Integration in the Life Sciences Springer. pp. 132-143
Ten simple rules for organizing a scientific meeting.
Corpas, M., Gehlenborg, N., Janga, S.C. and Bourne, P.E. 2008. Ten simple rules for organizing a scientific meeting. PLOS Computational Biology. 4 (6) e1000080. https://doi.org/10.1371/journal.pcbi.1000080
Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology
Gehlenborg, N., Corpas, M. and Janga, S.C. 2007. Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology. BMC Bioinformatics. 8 (Supplement 8) I1. https://doi.org/10.1186/1471-2105-8-s8-i1
PFF--an integrated database of residues and fragments critical for protein folding
Corpas, M., Sinnott, J., Thorne, D., Pettifer, S., Attwood , T. and the PFF consortium 2007. PFF--an integrated database of residues and fragments critical for protein folding. BMC Systems Biology. 1 P48. https://doi.org/10.1186/1752-0509-1-S1-P48
Scientists & societies: Community outreach
Corpas, M. 2005. Scientists & societies: Community outreach. Nature. 436, p. 1204. https://doi.org/10.1038/nj7054-1204b
Integrating simulation packages via systems biology mark-up language
Corpas, M. 2003. Integrating simulation packages via systems biology mark-up language. in: International Conference on Computational Methods in Systems Biology Springer.
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