Resources
Below is a list of resources produced by the Oxford Protein Informatics Group. This includes links to software written by group members as well as supplementary material associated with our papers. Resources are sorted by release date, with the most recent at the top.
Software & Databases (alphabetical order)
- ABDB: Antibody Structure Database [database]
- CSandS : Coding Sequence and Structure Database [database]
- FREAD [software download]
- FREAD [webserver]
- How Old Is Your Fold? [webserver]
- i-Patch [software download]
- i-Patch [webserver]
- iMembrane [webserver]
- JSUBST [software download]
- MEDELLER [webserver]
- THREADPAIR [software download]
All Resources (chronological order)
Environment-Specific Substitution Tables Improve Membrane Protein Alignment
Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
2011; Bioinformatics
- Substitution Tables (zip)
- JSUBST (zip)
- Paper
- THREADPAIR membrane protein sequence-to-structure alignment tool
MEDELLER: Homology-Based Coordinate Generation for Membrane Proteins
Sebastian Kelm, Jiye Shi and Charlotte M. Deane
2010 Oct 5; Bioinformatics
- MEDELLER web server
- Paper
- Supplementary material (pdf)
- Detailed benchmark tables (zip file containing OpenOffice Spreadsheets)
i-Patch: Inter-Protein Contact Prediction using Local Network Information
Rebecca Hamer, Qiang Luo, Judith P. Armitage, Gesine Reinert and Charlotte M. Deane
2010 Jun 10; Proteins
- Paper
- Download i-Patch (zip)
This software is free for academic use only. - i-Patch webserver
- Blind data alignments and structures (zip)
- Fitting data FASTA alignments (zip)
- Fitting data PDB structures (zip)
- Case study alignments (zip)
Signatures of Co-translational Folding
Rhodri Saunders, Martin Mann and Charlotte M. Deane
(submitted)
The Function of Communities in Protein Interaction Networks at Multiple Scales
A.C.F. Lewis, N.S.Jones, M.A.Porter and C.M.Deane
2010 Jul 22; BMC Syst. Biol.
Deciphering Chemotaxis Pathways Using Cross Species Comparisons
Rebecca Hamer, Pao-Yang Chen, Judith Armitage, Gesine Reinert and Charlotte M. Deane
2010 Jan 11; BMC Syst Biol.
FREAD Revisited: Database Search Loop Structure Prediction
Yoonjoo Choi and Charlotte M. Deane
2009 Oct 30; Proteins
Protein structure prediction begins well but ends badly
Rhodri Saunders, Charlotte M. Deane
2009 Oct 20; Proteins
iMembrane: Homology-based Membrane-Insertion of Proteins
Sebastian Kelm, Jiye Shi and Charlotte M. Deane
2009 Feb 23; Bioinformatics
Predicting and Validating Protein Interactions Using Network Structure
Pao-Yang Chen, Charlotte M. Deane and Gesine Reinert
2008 Jul 25; PLoS Comput Biol
A Statistical Approach Using Network Structure in The Prediction of Protein Characteristics
Pao-Yang Chen, Charlotte M. Deane and Gesine Reinert
2007 Jun 28; Bioinformatics
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