Resources
We maintain a number of webservers and databases which have their own websites, here are some useful links:
Codon language embeddings provide strong signals for protein engineering
Carlos Outeiral, Charlotte M. Deane
Paragraph - Antibody paratope prediction using Graph Neural Networks with minimal feature vectors
Lewis Chinery, Newton Wahome, Iain H. Moal, Charlotte M. Deane
AbLang: An antibody language model for completing antibody sequences
Tobias H. Olsen, Iain H. Moal, Charlotte M. Deane
Current structure predictors are not learning the physics of protein folding
Carlos Outeiral, Daniel A. Nissley, Charlotte M. Deane
Incorporating Target-Specific Pharmacophoric Information into Deep Generative Models for Fragment Elaboration
Thomas E. Hadfield, Fergus Imrie, Andy Merritt, Kristian Birchall, Charlotte M. Deane
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker
Constantin Schneider, Matthew I. J. Raybould, Charlotte M. Deane
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation
Brennan Abandes, Guy Georges, Alexander Bujotzek, Charlotte M. Deane
Humanization of antibodies using a machine learning approach on large-scale repertoire data
Claire Marks, Alissa M. Hummer, Mark Chin, Charlotte M. Deane
Epitope Profiling using Computational Structural Modelling, Demonstrated on Coronavirus-Binding Antibodies
Sarah A. Robinson and Matthew I.J. Raybould, Constantin Schneider, Wing Ki Wong, Claire Marks, Charlotte M. Deane
Deep Generative Design with 3D Pharmacophoric Constraints
Fergus Imrie, Thomas E Hadfield, Anthony R Bradley, Charlotte M Deane
Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained On Docked Poses
Fergus Boyles, Charlotte M Deane, Garrett Morris
Generating Property-Matched Decoy Molecules Using Deep Learning
Fergus Imrie, Anthony R Bradley, Charlotte M Deane
- Paper
- GitHub Repo
- Pretrained Models [Updated 28th Oct]
- Generated Decoys [Updated 28th Oct]
- Subgraph Frequency Data [Updated 28th Oct]
Robust gene coexpression networks using signed distance correlation
Javier Pardo-Diaz, Lyuba V Bozhilova, Mariano Beguerisse-Diaz, Philip S Poole, Charlotte M Deane, Gesine Reinert
A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-Pertussis toxoid antibodies
Eve Richardson, Jacob D. Galson, Dominic F. Kelly, Sarah E. Smith, Anne Palser, Simon Watson, Charlotte M. Deane
CoV-AbDab: the Coronavirus Antibody Database
Matthew I. J. Raybould, Aleksandr Kovaltsuk, Claire Marks, Charlotte M. Deane
- Paper
- Database
- Supplementary File 1 [from Preprint]
- Supplementary File 2 [from Preprint]
Ab-Ligity: Identifying sequence-dissimilar antibodies that bind to the same epitope
Wing Ki Wong, Sarah A. Robinson, Alexander Bujotzek, Guy Georges, Alan P. Lewis, Jiye Shi, James Snowden, Bruck Taddese, Charlotte M. Deane
Public Baseline and Shared Response Structures Support the Theory of Antibody Repertoire Functional Commonality
Matthew I. J. Raybould, Claire Marks, Aleksandr Kovaltsuk, Alan P. Lewis, Jiye Shi, Charlotte M. Deane
- Paper
- Dataset 1: Public Baseline FREAD Templates
- Dataset 2: Public Baseline Antibody Model Library
- Dataset 3: Public Baseline Fv Sequences
- Dataset 4: Public Response Antibody Model Library
BOKEI: Bayesian optimization using knowledge of correlated torsions and expected improvement for conformer generation
Lucian Chan, Geoffrey R. Hutchison, Garrett M. Morris
Structural Diversity of B-Cell Receptor Repertoires along the B-cell Differentiation Axis in Humans and Mice
Aleksandr Kovaltsuk, Matthew I. J. Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück, Charlotte M. Deane
TCRBuilder: Multi-state T-cell receptor structure prediction
Wing Ki Wong, Claire Marks, Jinwoo Leem, Alan P. Lewis, Jiye Shi and Charlotte M. Deane
Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks
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 I. J. 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
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions
Bernhard Knapp, Marta Alcala, Hao Zhang, Clare E. West, Anton van der Merwe, Charlotte M Deane
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
- Paper
- TAP Web Application
- Clinical-Stage Therapeutic Models
- Vander Heiden Human Ig-seq Models and corresponding sequences
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
- Paper
- Flib Source Code (.tgz)
- PDB-Representative Data Set (.tgz)
- CASP Data Set (.tgz)
- Training Data Set (.tgz)
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, 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, 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
- Paper
- Substitution Tables (zip)
- JSUBST (zip)
- THREADPAIR membrane protein sequence-to-structure alignment tool
MEDELLER: Homology-Based Coordinate Generation for Membrane Proteins
Sebastian Kelm, Jiye Shi, Charlotte M. Deane
- Paper
- Supplementary material (pdf)
- Detailed benchmark tables (zip file containing OpenOffice Spreadsheets)
- Medeller/iMembrane Source Code (tarball, in place of former web application)
i-Patch: Inter-Protein Contact Prediction using Local Network Information
Rebecca Hamer, Qiang Luo, Judith P. Armitage, Gesine Reinert, Charlotte M. Deane
- 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, Charlotte M. Deane
The Function of Communities in Protein Interaction Networks at Multiple Scales
A.C.F. Lewis, N.S.Jones, M.A.Porter, C.M.Deane
Deciphering Chemotaxis Pathways Using Cross Species Comparisons
Rebecca Hamer, Pao-Yang Chen, Judith Armitage, Gesine Reinert, Charlotte M. Deane
FREAD Revisited: Database Search Loop Structure Prediction
Yoonjoo Choi, 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, Charlotte M. Deane
- Paper
- Supplementary material (pdf)
- Medeller/iMembrane Source Code (tarball, in place of former web application)
Predicting and Validating Protein Interactions Using Network Structure
Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert
A Statistical Approach Using Network Structure in The Prediction of Protein Characteristics
Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert