Resources

We maintain a number of webservers and databases which have their own websites, linked to from the icons on his page. Other software downloads and supplementary material from papers are listed below, sorted by release date with the most recent at the top.

 

All Resources (chronological order)



Examining the conservation of kinks in alpha helices
Eleanor C. Law, Henry R. Wilman, Sebastian Kelm, Jiye Shi, Charlotte M. Deane [Submitted]


Kink Finder (Error estimation update)
Henry Wilman, Jiye Shi, and Charlotte M. Deane


ANARCI: Antigen receptor numbering and receptor classification
James Dunbar and Charlotte M. Deane [Submitted]


Structural bridges through fold space
Hannah Edwards and Charlotte M. Deane [Submitted]


Building a better fragment library for de novo protein structure prediction
Saulo H.P. de Oliveira, Jiye Shi, and Charlotte M. Deane


An Antibody-Specific, Knowledge-based Framework for Predicting Affinities
Jinwoo Leem, Jiye Shi, Guy Georges, Kanti V. Mardia, and Charlotte M. Deane [Submitted]


OOMMPPAA: A tool to aid directed synthesis by the combined analysis of activity and structural data
Anthony R. Bradley, Ian D. Wall, Darren V.S. Green, Charlotte M. Deane, Brian D. Marsden


Crowdsourcing yields a new standard for protein helix kinks
Henry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, Bernhard Knapp

Click on the link below to download a zip archive containing the gold standard helix annotation described in the paper. The archive also contains the raw data collected by AHAH.


Gro2mat: A package to efficiently read Gromacs output in Matlab
Hung Dien, Charlotte Deane, Bernhard Knapp


Helix kinks are equally prevalent in soluble and membrane proteins
Henry R. Wilman, Jiye Shi, Charlotte M. Deane

 

B-cell epitope prediction improves global antibody-antigen docking
Konrad Krawczyk, Terry Baker, Jiye Shi, Charlotte M. Deane


Kink Finder
Henry Wilman, Jiye Shi, and Charlotte M. Deane


Exploring fold space preferences of ancient and new-born protein superfamilies
Hannah Edwards, Sanne Abeln, Charlotte M. Deane.


Fragment-based modelling of membrane protein loops - successes, failures and prospects for the future
Sebastian Kelm, Anna Vangone, Yoonjoo Choi, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane.


ABangle
James Dunbar, Angelika Fuchs, Jiye Shi and Charlotte M. Deane. 2013. Protein Engineering, Design and Selection.

  

Antibody i-Patch predictions of the antibody binding site improve local rigid antibody-antigen docking
Konrad Krawczyk, Terry Baker, Jiye Shi, Charlotte M. Deane

 

MP-T: improving membrane protein alignment for structure prediction
Jamie R. Hill, Charlotte M. Deane

 

Environment-Specific Substitution Tables Improve Membrane Protein Alignment
Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
2011; Bioinformatics

 

MEDELLER: Homology-Based Coordinate Generation for Membrane Proteins
Sebastian Kelm, Jiye Shi and Charlotte M. Deane
2010 Oct 5; Bioinformatics

 

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

 

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