Resources and software

To support our research work we use a multitude of different technologies including software and systems built in-house. A list of available and downloadable resources and software can be found on this page.

These resources are for bioinformatic analysis of protein structure, biocatalysis design and the assembly of biochemical reaction pathways. External parties are also welcome to access these tools and applications.

• Protein-Sol is a webserver for predicting the solubility of proteins from primary sequence data, developed. It is also able to calculate protein surface charge and hydrophobicity.
  Reference: Hebditch M, Carballo-Amador MA, Charonis S, Curtis R, Warwicker J. Bioinformatics, 2017, 33, 3098.
• Retropath2.0 is used to explore the chemical biosynthetic space, RetroPath provides an automated open source workflow based on generalized reaction rules that performs retrosynthesis search from chassis to target through an efficient and well-controlled protocol.
  Reference: Delépine B, Duigou T, Carbonell P, Faulon JL. Metabolic Engineering, 2017, 45, 158; Koch M, Duigou T, Carbonell P, Faulon JL. Journal of Cheminformatics, 2017, 91, 64.
• SensiPath is a web server tool (co-developed with Micalis/INRA) to identify putative biochemical transformations of target compounds and allow identification of easily detectable compounds for screening and identification of potential biosensors.
  Reference: Delepine B, Libis V, Carbonell P, Faulon JL. Nucleic Acids Research, 2016, 44, W226.
• Selenzyme is an on line enzyme selection tool for target reactions or set of reactions for metabolic pathway design that allows us to mine candidate enzyme sequences for any desired target reaction or set of reactions in a pathway and the search for alternative routes or pathways leading to non-natural products. Selenzyme uses our biochem4j graph database as its main data source and provides bespoke sequence selection for automated workflows.
  Reference: Carbonell P, Wong J, Swainston N, Takano E, Turner NJ, Scrutton NS, Kell DB, Breitling R, Faulon JL. Bioinformatics, 2018, 34, 2153.
• Biochem4j is a freely available graph database of integrated chemical, reaction, enzyme and taxonomic data, based on the neo4j database. Biochem4j has applications in pathway elucidation, enzyme selection and metabolic modelling, acting as a knowledge base which brings together distributed data into an integrated and queryable system. It currently contains relevant information of known relationships between reactions (36765), chemicals (19735), enzymes (245704) and organisms (8431).
  Reference: Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon JL, Mendes P, Kell DB, Scrutton NS, Breitling R. PLOS One, 2017, 12, e0179130.
• PartsGenie is a web application for the design of reusable synthetic biology parts that offers simultaneous codon optimisation, RBS design, CDS RBS removal, assembly and synthesis compatibility. It is designed to bridge the gap between optimisation tools for the design of novel parts, the representation of such designs in community-developed data standards such as Synthetic Biology Open Language (SBOL), and the sharing of designs in journal-recommended data repositories (JBEI-ICE). It facilitates the design, optimisation and dissemination of reusable synthetic biology parts through a single, integrated application. PartsGenie has been used for the design of most synthetic DNA used in the SYNBIOCHEM Centre and elsewhere in the MIB and is now freely available to the wider synthetic biology community.
  Reference: Swainston N, Dunstan M, Jervis AJ, Robinson CJ, Carbonell P, Williams AR, Faulon JL, Scrutton NS, Kell DB. Bioinformatics,2018, 34, 2327.
• GeneGenie, SpeedyGenes and CodonGenie are a family of tools for designing genes in variant library design and directed evolution projects. GeneGenie supports the design and self-assembly of synthetic genes and constructs. SpeedyGenes, a PCR-based method for the synthesis of diverse protein libraries that includes an error-correction procedure, enabling the efficient synthesis of large genes for use directly in functional screening. CodonGenie will design and analyse all ambiguous codons that encode the required amino acids for the intended host organism.
  Reference: Swainston N, Currin A, Day PJ and Kell DB. Nucleic Acids Research, 2014, 42, W395; Currin A, Swainston N, Day PJ, Kell DB. Protein Engineering Design and Selection, 2017, 27, 273; Swainston N, Currin A, Green L, Breitling R, Day PJ, Kell DB. PeerJ Computer Science, 2017, 7, e120.
• CodonGenie is an application for designing ambiguous codons to support protein mutagenesis. Given a user-defined target collection of amino acids and an intended host organism, CodonGenie will design and analyse all ambiguous codons that encode the required amino acids. The codons are ranked according to their efficiency in encoding the required amino acids while minimising the encoding of additional amino acids and stop codons.
  Reference: Swainston N, Currin A, Green L, Breitling R, Day PJ, Kell DB. (2017). CodonGenie: optimised ambiguous codon design tools. PeerJ Computer Science, 7, e120. DOI: 10.7717/peerj-cs.120.