Resources

We maintain a number of webservers and databases which have their own websites, linked to from the publication list below. Other software downloads and supplementary material from papers are also available. All tools are sorted by release date with the most recent at the top.

 

Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks (Preprint)
Florian Klimm, Enrique M. Toledo, Thomas Monfeuga, Fang Zhang, Charlotte M. Deane, Gesine Reinert


Comparative analysis of the CDR loops of antigen receptors
Wing Ki Wong, Jinwoo Leem, Charlotte M. Deane


Thera-SAbDab: the Therapeutic Structural Antibody Database
Matthew IJ Raybould, Claire Marks, Alan P. Lewis, Jiye Shi, Alexander Bujotzek, Bruck Taddese, Charlotte M. Deane


RFQAmodel: Random Forest Quality Assessment to identify a predicted protein structure in the correct fold
Clare E. West, Saulo H.P. de Oliveira & Charlotte M. Deane


Learning From The Ligand: Using Ligand-Based Features To Improve Binding Affinity Prediction
Fergus Boyles, Charlotte M. Deane, Garrett M. Morris


Measuring rank robustness in scored protein interaction networks
Lyuba V. Bozhilova, Alan V. Whitmore, Jonny Wray, Gesine Reinert, Charlotte M. Deane


Five Computational Developability Guidelines for Therapeutic Antibody Profiling
Matthew I.J. Raybould, Claire Marks, Konrad Krawczyk, Bruck Taddese, Jaroslaw Nowak, Alan P. Lewis, Alexander Bujotzek, Jiye Shi, Charlotte M. Deane


Observed Antibody Space: a resource for data mining next generation sequencing antibody repertoires
Aleksandr Kovaltsuk, Jinwoo Leem, Sebastian Kelm, James Snowden, Charlotte M. Deane, Konrad Krawczyk


SCALOP: sequence-based antibody canonical loop structure prediction
Wing Ki Wong, Guy Georges, Francesca Ros, Sebastian Kelm, Alan P. Lewis, Bruck Taddese, Jinwoo Leem and Charlotte M. Deane


ABOSS, filtering Ig-seq data with structural information
Aleksandr Kovaltsuk, Konrad Krawczyk, Sebastian Kelm, James Snowden and Charlotte M. Deane


Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction
Saulo H.P. de Oliveira, Eleanor C. Law, Jiye Shi & Charlotte M. Deane


Combining co-evolution and secondary structure prediction to improve fragment library generation
Saulo H.P. de Oliveira, Charlotte M. Deane


A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density
Nicholas M. Pearce, Tobias Krojer, Anthony R. Bradley, Patrick Collins, Radosław P. Nowak, Romain Talon, Brian D. Marsden, Sebastian Kelm, Jiye Shi, Charlotte M. Deane & Frank von Delft


CommWalker: correctly evaluating modules in molecular networks in light of annotation bias
Malte D. Luecken, Matthew J. T. Page, Andrea J. Crosby, Sean Mason, Gesine Reinert, Charlotte M. Deane


Identifying networks with common organizational principles
Anatol E. Wegner, Luis Ospina-Forero, Robert E. Gaunt, Charlotte M. Deane, Gesine Reinert


Identifying reproducible ribo-seq data at the codon-level
Alistair Martin, Charlotte M. Deane


Comparing co-evolution methods and their application to template-free protein structure prediction
Saulo H.P. de Oliveira, Jiye Shi, Charlotte M. Deane


ABodyBuilder: Automated antibody structure prediction with data–driven accuracy estimation
Jinwoo Leem, James Dunbar, Guy Georges, Jiye Shi, Charlotte M. Deane


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


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


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


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


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


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

 

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

 

i-Patch: Inter-Protein Contact Prediction using Local Network Information
Rebecca Hamer, Qiang Luo, Judith P. Armitage, Gesine Reinert and Charlotte M. Deane

 

Signatures of Co-translational Folding
Rhodri Saunders, Martin Mann and Charlotte M. Deane

 

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

 

Deciphering Chemotaxis Pathways Using Cross Species Comparisons
Rebecca Hamer, Pao-Yang Chen, Judith Armitage, Gesine Reinert and Charlotte M. Deane

 

FREAD Revisited: Database Search Loop Structure Prediction
Yoonjoo Choi and Charlotte M. Deane

 

Protein structure prediction begins well but ends badly
Rhodri Saunders, Charlotte M. Deane

 

iMembrane: Homology-based Membrane-Insertion of Proteins
Sebastian Kelm, Jiye Shi and Charlotte M. Deane

 

Predicting and Validating Protein Interactions Using Network Structure
Pao-Yang Chen, Charlotte M. Deane and Gesine Reinert

 

A Statistical Approach Using Network Structure in The Prediction of Protein Characteristics
Pao-Yang Chen, Charlotte M. Deane and Gesine Reinert