Ralf Schmid

Ralf Schmid Tel: +44 (0)116 229 7023

 

Personal details

  • PhD: Albert-Ludwigs-Universitat Freiburg 2000
  • Postdoctoral Research Fellow, Albert-Ludwigs-Universitat Freiburg 2000-01
  • Postdoctoral Research Fellow, University of Edinburgh 2001-05
  • Lecturer in Bioinformatics, University of Leicester 2006-2016
  • Associate Professor, University of Leicester 2016-present

Publications

  1. Winter A, Schmid R, Bayliss R. (2015) Structural Insights into Separase Architecture and Substrate Recognition through computational modelling of Caspase-like and Death domains. PLoS Computational Biology11(10), e10045489. link
  2. Farmer LK, Schmid R, Evans RJ. (2015) Use of Chimeras, Point Mutants, and Molecular Modeling to Map the Antagonist-binding Site of 4,4',4,4‴-(Carbonylbis-(imino-5,1,3-benzenetriylbis(carbonylimino)))tetrakisbenzene-1,3-disulfonic Acid (NF449) at P2X1 Receptors for ATP.Journal of Biological Chemistry290, 1559-69. link
  3. Graciotti M, Alam, M, Solyakov L, Schmid R, Burley G, Bottrill AR, Doerig C, Cullis P, Tobin AB. (2014) Malaria Protein Kinase CK2 (PfCK2) Shows Novel Mechanisms of Regulation.. PLoS One9(3), e85391. link
  4. Pegoraro M, Noreen S, Bhutani S, Tsolou A, Schmid R, Kyriacou CP, Tauber E. (2014) Molecular Evolution of a Pervasive Natural Amino-Acid Substitution in Drosophila cryptochrome. PLoS One9(1), e86483. link
  5. Popovics P, Jin L, Kamil LN, Morgan K, Millar RP, Schmid R, Blindauer CA, Stewart AJ. (2014) A canonical EF-loop directs Ca2+-sensitivity in phospholipase C-η2. Journal of Cellular Biochemistry115, 557-565. link
  6. Schmid R, Grellscheid SN, Ehrmann I, Dalgliesh C, Danilenko M, Paronetto MP, Pedrotti S, Grellscheid D, Dixon RJ, Sette C, Eperon IC, Elliott DJ. (2013) The splicing landscape is globally reprogrammed during male meiosis. Nucleic Acids Research41 10170-84. link
  7. Shafiq MI, Steinbrecher T, Schmid R. (2012) FASCAPLYSIN as a Specific Inhibitor for CDK4: Insights from Molecular Modelling. PLoS One7(8), e42612. link
  8. Barnett JP, Millard A, Ksibe AZ, Scanlan DJ, Schmid R, Blindauer CA. (2012) Mining genomes of marine cyanobacteria for elements of zinc homeostasis. Frontiers in Microbiology3, 142. link
  9. Roberts JA, Allsopp RC, El Ajouz S, Vial C, Schmid R, Young MT, Evans RJ. (2012) Agonist binding evokes extensive conformational changes in the extracellular domain of the ATP-gated human P2X1 receptor ion channel Proceedings of the National Academy of Science U.S.A.109, 4663-4667. link
  10. Rieck B, Tourigny DS, Crosatti M, Schmid R, Kochar M, Harrison EM, Ou HY, Turton JF Rajakumar K. (2012) Acinetobacter Insertion Sequence ISAba11 Belongs to a Novel Family That Encodes Transposases with a Signature HHEK Motif. Applied and Environmental Microbiology78, 471-480. link
  11. Allsopp RC, El Ajouz S, Schmid R, Evans RJ. (2011) Cysteine Scanning Mutagenesis (Residues Glu(52)-Gly(96)) of the Human P2X1 Receptor for ATP: Mapping Agonist Binding and Channel Gating Journal of Biological Chemistry286, 29207-29217. link
  12. Blindauer CA, Schmid R. (2010) Cytosolic metal handling in plants: determinants for zinc specificity in metal transporters and metallothioneins. Metallomics2, 510-529. link
  13. Wallis R, Mitchell DA, Schwaeble WJ, Schmid R, Keeble AH. (2010) Paths reunited: activation of the classical and lectin pathways of complement. Immunobiology215, 1-11. link
  14. Grant-Downton R, Le Trionnaire G, Schmid R, Rodriguez-Enriquez J, Hafidh S, Mehdi S, Twell D, Dickinson H. (2009) MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thalianaBMC Genomics,10, 643. link
  15. Cai H, Sale S, Schmid R, Britton RG, Brown K, Steward WP, Gescher AJ. (2009) Flavones as colorectal cancer chemopreventive agents - phenol-O-methylation enhances efficacy. Cancer Prevention Research, 2, 743-750. link
  16. Phillips AE, Toth J, Dodds AW, Venkatraman Girija U, Furze C, Pala E, Sim RB, Reid KBM, Schwaeble WJ, Schmid R, Keeble AH, Wallis R. (2009) Analogous Interactions in Initiating Complexes of the Classical and Lectin Pathways of Complement. Journal of Immunology182, 7708-7717. link
  17. Schmid R, Blaxter ML. (2009) EST processing: from trace to sequence. Methods in Molecular Biology533, 189-220. link
  18. Schmid R. (2008) Pitfalls of using out of date databases - Comment on Guo et al. and Guo et alJournal of Theoretical Biology255, 262. link
  19. Menz B, Sester M, Koebernick K, Schmid R, Burgert H-G. (2008) Structural analysis of the adenovirus type 2 E3/19K protein using mutagenesis and a panel of conformation-sensitive monoclonal antibodies. Molecular Immunology46, 16-26. link
  20. Wasmuth JW, Schmid R, Hedley A, Blaxter ML. (2008) On the extent and origins of genic novelty in the phylum Nematoda. PLoS Neglected Tropical Diseases2(7), e258. link
  21. Schmid R, Blaxter ML. (2008) annot8r: GO, EC and KEGG annotation of EST datasets. BMC Bioinformatics9, 180. link
  22. Chalmers IW, McArdle AJ, Coulson RMR, Wagner MA, Schmid R, Hirai H, Hoffmann KF. (2008) Developmentally regulated expression, alternative splicing and distinct sub-groupings in members of the Schistosoma mansoni venom allergen-like (SmVAL) gene family. BMC Genomics,9, 89. link
  23. Leszczyszyn OI, Schmid R, Blindauer CA. (2007) Toward a property/function relationship for metallothioneins: Histidine coordination and unusual cluster composition in a zinc-metallothionein from plants. Proteins-Structure Function and Bioinformatics, 68, 922-935. link
  24. Roberts SJ, Stewart AJ, Schmid R, Blindauer CA, Bond SR, Sadler PJ, Farquharson C. (2005) Probing the substrate specificities of human PHOSPHO1 and PHOSPHO2. Biochimica Biophysica Acta1752, 73-82. link
  25. Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, Martin J, Schmid R, Hall N, Waterston RH, McCarter JP, Blaxter ML. (2004) A Transcriptomic Analysis of the Phylum Nematoda. Nature Genetics36, 1259-1267. link
  26. Schmid R, Gerloff DL. (2004) Functional properties of the alternative NADH:ubiquinone oxidoreductase from E. coli through comparative 3-D modelling. FEBS Letters578, 163-168. link
  27. Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, Blaxter M. (2004) PartiGene – constructing partial genomes. Bioinformatics20, 1398-1404. link
  28. Borrelly GPM, Blindauer CA, Schmid R, Butler CS, Cooper CE, Harvey I, Sadler PJ, Robinson NJ. (2004) A novel copper site in a cyanobacterial metallochaperone (Accelerated Publication). Biochemical Journal378, 293-297. link
  29. Parkinson J, Whitton C, Schmid R, Thomson M, Blaxter M. (2004) NEMBASE: a resource for parasitic nematode ESTs. Nucleic Acid Research32, D427-D430. link
  30. Stewart AJ, Schmid R, Blindauer CA, Paisey SJ, Farquharson C. (2003) Comparative modelling of human PHOSPHO1 reveals a new group of phosphatases within the HAD superfamily. Protein Engineering16, 889-895. link
  31. Hucke O, Schmid R, Labahn A. (2002) Exploring the primary electron acceptor (QA)-site of the bacterial reaction center from Rhodobacter sphaeroides : binding mode of vitamin K derivatives. European Journal of Biochemistry269, 1096-1108. link
  32. Schmid R, Labahn A. (2000) Temperature and free energy dependence of the direct charge recombination rate from the secondary quinone in bacterial reaction centers from Rhodobacter sphaeroidesJournal of Physical Chemistry B104, 2928-2936. link
  33. Schmid R. (2000) Untersuchung von Elektronentransferreaktionen in photosynthetischen Reaktionszentren. Logos Verlag Berlin, ISBN 978-3-89722-195-6. link
  34. Schmid R, Goebel F, Warnecke A, Labahn A. (1999) Synthesis and redox potentials of methylated vitamin K derivatives. Journal of the Chemical Society Perkin Transactions 26, 1199-1202. link
  35. Labahn A, Schmid R, Okamura MY, Feher G (1998) Temperature dependence of the direct charge recombination from QB-· to D+ in bacterial reaction centers of Rhodobacter sphaeroides. Photosynthesis: Mechanisms and EffectsVol. II, G. Garab (Ed.); Kluwer Academic Publishers, Netherlands, 829-832.
  36. Schmid R, Labahn A. (1998) The influence of quinone structure on quinone binding to the QA-site in bacterial reaction centers from Rhodobacter sphaeroides. Photosynthesis: Mechanisms and EffectsVol. III, G. Garab (Ed.); Kluwer Academic Publishers, Netherlands, 877-880.

For metrics etc. see publications on ResearcherID.

Research

  • Protein structure prediction
  • Docking methods
  • Molecular dynamics simulations
  • Sequence analysis
  • Comparative genomics
  • Evolution of protein families
  • Bioenergetics

Supervision

Group members - the team

Ralf Schmid

RS is a bioinformatician coming from a biophysical chemistry background. His main interest is in protein structure/function/interaction and he attempts to address biological questions related to this from a joint evolutionary and biophysics perspective (see publications for recent examples).

He codes mostly in Perl as his java is a bit rusty and his python not as far developed as he anticipated a year ago. He enjoys messing around with data and trying to keep up with science in general and molecular modelling &bioinformatics research in particular.

He is (almost) always happy to give bioinformatics advice (if in his fields of expertise) and to explore scope for new collaborations.

Sudad Dayl

Sudad has an undergraduate BSc Chemistry degree from the University of Baghdad and a Masters in Bioinformatics degree from the University of Leicester.

Sudad joined the group in 2014 on a studentship from the Higher Committee for Education Development in Iraq (HCED). His PhD project focuses on different aspects of molecular modelling of P2X receptors.

After one year in the group he is a proficient user of homology modelling, ligand docking, molecular dynamics simulations and even manages to get rosetta to do what he wants.

You...

At the moment we have no funded PhD or postdoc positions available. However, if you are interested in working with us and have - or may be able to acquire - your own funding, feel free to get in touch to discuss potential projects.

Alumni

Imtiaz M Shafiq (PhD 2011)

Imtiaz joined the group in 2007 on a grant from HEC Pakistan. His PhD project focused on homology modelling, ligand docking and structure based drug design for specific CDK4 inhibitors (in collaboration with Paul Jenkins from Chemistry).

Imtiaz is now an Assistant Professor at the University of Punjab, Lahore,

Abbas Alameer (PhD 2013)

Abbas came on a PhD studentship funded by the University of Kuwait and worked with us (and Mark Carr's group) on using RDC and other NMR data combined with constraints derived from evolutionary considerations to improve in silico protein-protein docking, and developed the PROTIN tool.

After finishing his PhD, Abbas went back to the University of Kuwait to start his own Bioinformatics research group.

Share this page:

Contact Details

Department of Molecular and Cell Biology
Henry Wellcome Building
Lancaster Road
Leicester
LE1 7RH (Postal)

LE1 7HB (Sat Nav/Online maps)

T:  +44(0)116 229 7038
F:  +44(0)116 229 7123
MolCellBiol@le.ac.uk

Accessibility

DisabledGo logo

The University of Leicester is committed to equal access to our facilities. DisabledGo has a detailed accessibility guide for the Henry Wellcome Building.

Redfearn Lecture 2017

To Be Confirmed