Charlotte M. Deane

ORCID

Publication Activity (10 Years)

Years Active: 1998-2024
Publications (10 Years): 69

Top Venues

Publications

Carlos Outeiral, Charlotte M. Deane
Codon language embeddings provide strong signals for use in protein engineering. Nat. Mac. Intell. 6 (2) (2024)
Leo Klarner, Tim G. J. Rudner, Garrett M. Morris, Charlotte M. Deane, Yee Whye Teh
Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design. CoRR (2024)
Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane
Large scale paired antibody language models. CoRR (2024)
Henry Kenlay, Frédéric A. Dreyer, Daniel Cutting, Daniel A. Nissley, Charlotte M. Deane
ABodyBuilder3: Improved and scalable antibody structure predictions. CoRR (2024)
Anna Carbery, Martin Buttenschoen, Rachael Skyner, Frank von Delft, Charlotte M. Deane
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures. J. Cheminformatics 16 (1) (2024)
Daniel Cutting, Frédéric A. Dreyer, David Errington, Constantin Schneider, Charlotte M. Deane
De novo antibody design with SE(3) diffusion. CoRR (2024)
Jack Scantlebury, Lucy Vost, Anna Carbery, Thomas E. Hadfield, Oliver M. Turnbull, Nathan Brown, Vijil Chenthamarakshan, Payel Das, Harold Grosjean, Frank von Delft, Charlotte M. Deane
A Small Step Toward Generalizability: Training a Machine Learning Scoring Function for Structure-Based Virtual Screening. J. Chem. Inf. Model. 63 (10) (2023)
Maranga Mokaya, Fergus Imrie, Willem P. van Hoorn, Aleksandra Kalisz, Anthony R. Bradley, Charlotte M. Deane
Testing the limits of SMILES-based de novo molecular generation with curriculum and deep reinforcement learning. Nat. Mac. Intell. 5 (4) (2023)
Stephanie Wills, Ruben Sanchez-Garcia, Tim Dudgeon, Stephen D. Roughley, Andy Merritt, Roderick E. Hubbard, James Davidson, Frank von Delft, Charlotte M. Deane
Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search. J. Chem. Inf. Model. 63 (11) (2023)
Thomas E. Hadfield, Jack Scantlebury, Charlotte M. Deane
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding. J. Cheminformatics 15 (1) (2023)
Leo Klarner, Tim G. J. Rudner, Michael Reutlinger, Torsten Schindler, Garrett M. Morris, Charlotte M. Deane, Yee Whye Teh
Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions. ICML (2023)
Frédéric A. Dreyer, Daniel Cutting, Constantin Schneider, Henry Kenlay, Charlotte M. Deane
Inverse folding for antibody sequence design using deep learning. CoRR (2023)
Szabolcs Elias, Clemens Wrzodek, Charlotte M. Deane, Alain C. Tissot, Stefan Klostermann, Francesca Ros
Prediction of polyspecificity from antibody sequence data by machine learning. Frontiers Bioinform. 3 (2023)
Lewis Chinery, Newton Wahome, Iain Moal, Charlotte M. Deane
Paragraph - antibody paratope prediction using graph neural networks with minimal feature vectors. Bioinform. 39 (1) (2023)
Valentin J. Hoerschinger, Franz Waibl, Nancy D. Pomarici, Johannes R. Loeffler, Charlotte M. Deane, Guy Georges, Hubert Kettenberger, Monica L. Fernández-Quintero, Klaus R. Liedl
PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability. J. Chem. Inf. Model. 63 (22) (2023)
Leo Klarner, Tim G. J. Rudner, Michael Reutlinger, Torsten Schindler, Garrett M. Morris, Charlotte M. Deane, Yee Whye Teh
Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions. CoRR (2023)
Carlos Outeiral, Daniel A. Nissley, Charlotte M. Deane
Current structure predictors are not learning the physics of protein folding. Bioinform. 38 (7) (2022)
Fergus Boyles, Charlotte M. Deane, Garrett M. Morris
Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained on Docked Poses. J. Chem. Inf. Model. 62 (22) (2022)
Constantin Schneider, Matthew I. J. Raybould, Charlotte M. Deane
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker. Nucleic Acids Res. 50 (D1) (2022)
Javier Pardo-Diaz, Philip S. Poole, Mariano Beguerisse-Díaz, Charlotte M. Deane, Gesine Reinert
Generating weighted and thresholded gene coexpression networks using signed distance correlation. Netw. Sci. 10 (2) (2022)
James B. Wilsenach, Catherine E. Warnaby, Charlotte M. Deane, Gesine D. Reinert
Ranking of Communities in Multiplex Spatiotemporal Models of Brain Dynamics. CoRR (2022)
James B. Wilsenach, Catherine E. Warnaby, Charlotte M. Deane, Gesine Reinert
Ranking of communities in multiplex spatiotemporal models of brain dynamics. Appl. Netw. Sci. 7 (1) (2022)
Javier Pardo-Diaz, Mariano Beguerisse-Díaz, Philip S. Poole, Charlotte M. Deane, Gesine Reinert
. J. Comput. Biol. 29 (7) (2022)
Thomas E. Hadfield, Fergus Imrie, Andy Merritt, Kristian Birchall, Charlotte M. Deane
Incorporating Target-Specific Pharmacophoric Information into Deep Generative Models for Fragment Elaboration. J. Chem. Inf. Model. 62 (10) (2022)
Constantin Schneider, Andrew Buchanan, Bruck Taddese, Charlotte M. Deane
DLAB: deep learning methods for structure-based virtual screening of antibodies. Bioinform. 38 (2) (2022)
Brennan Abanades, Guy Georges, Alexander Bujotzek, Charlotte M. Deane
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation. Bioinform. 38 (7) (2022)
Javier Pardo-Diaz, Lyuba V. Bozhilova, Mariano Beguerisse-Díaz, Philip S. Poole, Charlotte M. Deane, Gesine Reinert
Robust gene coexpression networks using signed distance correlation. Bioinform. 37 (14) (2021)
Dominik Schwarz, Guy Georges, Sebastian Kelm, Jiye Shi, Anna Vangone, Charlotte M. Deane
Co-evolutionary distance predictions contain flexibility information. Bioinform. 38 (1) (2021)
Lyuba V. Bozhilova, Javier Pardo-Diaz, Gesine Reinert, Charlotte M. Deane
COGENT: evaluating the consistency of gene co-expression networks. Bioinform. 37 (13) (2021)
Daniel A. Nissley, Anna Carbery, Mark Chonofsky, Charlotte M. Deane
Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains. Bioinform. 37 (13) (2021)
Matthew I. J. Raybould, Claire Marks, Aleksandr Kovaltsuk, Alan P. Lewis, Jiye Shi, Charlotte M. Deane
Public Baseline and shared response structures support the theory of antibody repertoire functional commonality. PLoS Comput. Biol. 17 (3) (2021)
Sarah A. Robinson, Matthew I. J. Raybould, Constantin Schneider, Wing Ki Wong, Claire Marks, Charlotte M. Deane
Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies. PLoS Comput. Biol. 17 (12) (2021)
Claire Marks, Alissa M. Hummer, Mark Chin, Charlotte M. Deane
Humanization of antibodies using a machine learning approach on large-scale repertoire data. Bioinform. 37 (22) (2021)
Florian Klimm, Charlotte M. Deane, Gesine Reinert
Hypergraphs for predicting essential genes using multiprotein complex data. J. Complex Networks 9 (2) (2021)
Fergus Imrie, Anthony R. Bradley, Charlotte M. Deane
Generating property-matched decoy molecules using deep learning. Bioinform. 37 (15) (2021)
Matthew I. J. Raybould, Aleksandr Kovaltsuk, Claire Marks, Charlotte M. Deane
CoV-AbDab: the coronavirus antibody database. Bioinform. 37 (5) (2021)
Fergus Boyles, Charlotte M. Deane, Garrett M. Morris
Learning from the ligand: using ligand-based features to improve binding affinity prediction. Bioinform. 36 (3) (2020)
Aleksandr Kovaltsuk, Matthew I. J. Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück, Charlotte M. Deane
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice. PLoS Comput. Biol. 16 (2) (2020)
Wing Ki Wong, Claire Marks, Jinwoo Leem, Alan P. Lewis, Jiye Shi, Charlotte M. Deane
TCRBuilder: multi-state T-cell receptor structure prediction. Bioinform. 36 (11) (2020)
Mark Chonofsky, Saulo Henrique Pires de Oliveira, Konrad Krawczyk, Charlotte M. Deane
The evolution of contact prediction: evidence that contact selection in statistical contact prediction is changing. Bioinform. 36 (6) (2020)
Jack Scantlebury, Nathan Brown, Frank von Delft, Charlotte M. Deane
Data Set Augmentation Allows Deep Learning-Based Virtual Screening to Better Generalize to Unseen Target Classes and Highlight Important Binding Interactions. J. Chem. Inf. Model. 60 (8) (2020)
Fergus Imrie, Anthony R. Bradley, Mihaela van der Schaar, Charlotte M. Deane
Deep Generative Models for 3D Linker Design. J. Chem. Inf. Model. 60 (4) (2020)
Matthew I. J. Raybould, Claire Marks, Alan P. Lewis, Jiye Shi, Alexander Bujotzek, Bruck Taddese, Charlotte M. Deane
Thera-SAbDab: the Therapeutic Structural Antibody Database. Nucleic Acids Res. 48 (Database-Issue) (2020)
Lyuba V. Bozhilova, Alan Whitmore, Jonny Wray, Gesine Reinert, Charlotte M. Deane
Measuring rank robustness in scored protein interaction networks. BMC Bioinform. 20 (1) (2019)
Wing Ki Wong, Guy Georges, Francesca Ros, Sebastian Kelm, Alan P. Lewis, Bruck Taddese, Jinwoo Leem, Charlotte M. Deane
SCALOP: sequence-based antibody canonical loop structure annotation. Bioinform. 35 (10) (2019)
Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary
HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo. J. Chem. Inf. Model. 59 (6) (2019)
Luis Ospina-Forero, Charlotte M. Deane, Gesine Reinert
Assessment of model fit via network comparison methods based on subgraph counts. J. Complex Networks 7 (2) (2019)
Jean-Paul Ebejer, Paul W. Finn, Wing Ki Wong, Charlotte M. Deane, Garrett M. Morris
Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening. J. Chem. Inf. Model. 59 (6) (2019)
Bernhard Knapp, P. Anton van der Merwe, Omer Dushek, Charlotte M. Deane
MHC binding affects the dynamics of different T-cell receptors in different ways. PLoS Comput. Biol. 15 (9) (2019)
Claire Marks, Charlotte M. Deane
Increasing the accuracy of protein loop structure prediction with evolutionary constraints. Bioinform. 35 (15) (2019)
Saulo Henrique Pires de Oliveira, Eleanor C. Law, Jiye Shi, Charlotte M. Deane
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction. Bioinform. 34 (7) (2018)
Anatol E. Wegner, Luis Ospina-Forero, Robert E. Gaunt, Charlotte M. Deane, Gesine Reinert
Identifying networks with common organizational principles. J. Complex Networks 6 (6) (2018)
Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary
In silico structural modeling of multiple epigenetic marks on DNA. Bioinform. 34 (1) (2018)
Bernhard Knapp, Marta Alcalá, Hao Zhang, Clare E. West, P. Anton van der Merwe, Charlotte M. Deane
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions. Bioinform. 34 (11) (2018)
Fergus Imrie, Anthony R. Bradley, Mihaela van der Schaar, Charlotte M. Deane
Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data. J. Chem. Inf. Model. 58 (11) (2018)
Saulo Henrique Pires de Oliveira, Charlotte M. Deane
Combining co-evolution and secondary structure prediction to improve fragment library generation. Bioinform. 34 (13) (2018)
Malte Lücken, M. J. T. Page, A. J. Crosby, S. Mason, Gesine Reinert, Charlotte M. Deane
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias. Bioinform. 34 (6) (2018)
Jinwoo Leem, Saulo Henrique Pires de Oliveira, Konrad Krawczyk, Charlotte M. Deane
STCRDab: the structural T-cell receptor database. Nucleic Acids Res. 46 (Database-Issue) (2018)
Claire Marks, Jiye Shi, Charlotte M. Deane
Predicting loop conformational ensembles. Bioinform. 34 (6) (2018)
Samuel Demharter, Nicholas Pearce, Kylie Beattie, Isabel Frost, Jinwoo Leem, Alistair Martin, Robert Oppenheimer, Cristian Regep, Tammo Rukat, Alexander Skates, Nicola Trendel, David J. Gavaghan, Charlotte M. Deane, Bernhard Knapp
Ten simple rules for surviving an interdisciplinary PhD. PLoS Comput. Biol. 13 (5) (2017)
Anatol E. Wegner, Luis Ospina-Forero, Robert E. Gaunt, Charlotte M. Deane, Gesine Reinert
Identifying networks with common organizational principles. CoRR (2017)
Saulo Henrique Pires de Oliveira, Jiye Shi, Charlotte M. Deane
Comparing co-evolution methods and their application to template-free protein structure prediction. Bioinform. 33 (3) (2017)
Claire Marks, Jaroslaw Nowak, Stefan Klostermann, Guy Georges, James Dunbar, Jiye Shi, Sebastian Kelm, Charlotte M. Deane
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinform. 33 (9) (2017)
Konrad Krawczyk, Adelene Y. L. Sim, Bernhard Knapp, Charlotte M. Deane, Peter Minary
Tertiary Element Interaction in HIV-1 TAR. J. Chem. Inf. Model. 56 (9) (2016)
Bernhard Knapp, Samuel Demharter, Charlotte M. Deane, Peter Minary
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo. Bioinform. 32 (2) (2016)
Bernhard Knapp, Charlotte M. Deane
T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex. J. Chem. Inf. Model. 56 (1) (2016)
James Dunbar, Konrad Krawczyk, Jinwoo Leem, Claire Marks, Jaroslaw Nowak, Cristian Regep, Guy Georges, Sebastian Kelm, Bojana Popovic, Charlotte M. Deane
SAbPred: a structure-based antibody prediction server. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Reyhaneh Esmaielbeiki, Konrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane
Progress and challenges in predicting protein interfaces. Briefings Bioinform. 17 (1) (2016)
James Dunbar, Charlotte M. Deane
ANARCI: antigen receptor numbering and receptor classification. Bioinform. 32 (2) (2016)
Bernhard Knapp, Rémi Bardenet, Miguel O. Bernabeu, Rafel Bordas, Maria Bruna, Ben Calderhead, Jonathan Cooper, Alexander G. Fletcher, Derek Groen, Bram Kuijper, Joanna Lewis, Greg J. McInerny, Timo Minssen, James M. Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A. Yates, David Gavaghan, Charlotte M. Deane
Ten Simple Rules for a Successful Cross-Disciplinary Collaboration. PLoS Comput. Biol. 11 (4) (2015)
Anthony R. Bradley, Ian D. Wall, Frank von Delft, Darren V. S. Green, Charlotte M. Deane, Brian D. Marsden
WONKA: objective novel complex analysis for ensembles of protein-ligand structures. J. Comput. Aided Mol. Des. 29 (10) (2015)
Hannah Edwards, Charlotte M. Deane
Structural Bridges through Fold Space. PLoS Comput. Biol. 11 (9) (2015)
Bernhard Knapp, Samuel Demharter, Reyhaneh Esmaielbeiki, Charlotte M. Deane
Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations. Briefings Bioinform. 16 (6) (2015)
James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M. Deane
Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design. PLoS Comput. Biol. 10 (9) (2014)
James Dunbar, Konrad Krawczyk, Jinwoo Leem, Terry Baker, Angelika Fuchs, Guy Georges, Jiye Shi, Charlotte M. Deane
SAbDab: the structural antibody database. Nucleic Acids Res. 42 (Database-Issue) (2014)
Anthony R. Bradley, Ian D. Wall, Darren V. S. Green, Charlotte M. Deane, Brian D. Marsden
OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data. J. Chem. Inf. Model. 54 (10) (2014)
Hung Dien, Charlotte M. Deane, Bernhard Knapp
Gro2mat: A package to efficiently read gromacs output in MATLAB. J. Comput. Chem. 35 (20) (2014)
Bernhard Knapp, James Dunbar, Charlotte M. Deane
Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study. PLoS Comput. Biol. 10 (8) (2014)
Konrad Krawczyk, Xiaofeng Liu, Terry Baker, Jiye Shi, Charlotte M. Deane
Improving B-cell epitope prediction and its application to global antibody-antigen docking. Bioinform. 30 (16) (2014)
James M. Osborne, Miguel O. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G. Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J. McInerny, Gary R. Mirams, Joe Pitt-Francis, Biswa Sengupta, David W. Wright, Christian A. Yates, David Gavaghan, Stephen Emmott, Charlotte M. Deane
Ten Simple Rules for Effective Computational Research. PLoS Comput. Biol. 10 (3) (2014)
Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane
Alignment-free protein interaction network comparison. Bioinform. 30 (17) (2014)
Henry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, Bernhard Knapp
Crowdsourcing Yields a New Standard for Kinks in Protein Helices. J. Chem. Inf. Model. 54 (9) (2014)
Jean-Paul Ebejer, Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
Memoir: template-based structure prediction for membrane proteins. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Hannah Edwards, Sanne Abeln, Charlotte M. Deane
Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies. PLoS Comput. Biol. 9 (11) (2013)
Jamie R. Hill, Charlotte M. Deane
MP-T: improving membrane protein alignment for structure prediction. Bioinform. 29 (1) (2013)
Tiago Rito, Charlotte M. Deane, Gesine Reinert
The Importance of Age and High Degree, in Protein-Protein Interaction Networks. J. Comput. Biol. 19 (6) (2012)
Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte M. Deane
Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains. Adv. Bioinformatics 2012 (2012)
Anna C. F. Lewis, Nick S. Jones, Mason A. Porter, Charlotte M. Deane
What Evidence Is There for the Homology of Protein-Protein Interactions? PLoS Comput. Biol. 8 (9) (2012)
Jean-Paul Ebejer, Garrett M. Morris, Charlotte M. Deane
Freely Available Conformer Generation Methods: How Good Are They? J. Chem. Inf. Model. 52 (5) (2012)
Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
Environment specific substitution tables improve membrane protein alignment. Bioinform. 27 (13) (2011)
Jonathan J. Ellis, Fabien P. E. Huard, Charlotte M. Deane, Sheenal Srivastava, Graham R. Wood
Directionality in protein fold prediction. BMC Bioinform. 11 (2010)
Braddon K. Lance, Charlotte M. Deane, Graham R. Wood
Exploring the potential of template-based modelling. Bioinform. 26 (15) (2010)
Tiago Rito, Zi Wang, Charlotte M. Deane, Gesine Reinert
How threshold behaviour affects the use of subgraphs for network comparison. Bioinform. 26 (18) (2010)
Sumeet Agarwal, Charlotte M. Deane, Mason A. Porter, Nick S. Jones
Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks. PLoS Comput. Biol. 6 (6) (2010)
Rebecca Hamer, Pao-Yang Chen, Judith P. Armitage, Gesine Reinert, Charlotte M. Deane
Deciphering chemotaxis pathways using cross species comparisons. BMC Syst. Biol. 4 (2010)
Anna C. F. Lewis, Nick S. Jones, Mason A. Porter, Charlotte M. Deane
The function of communities in protein interaction networks at multiple scales. BMC Syst. Biol. 4 (2010)
Sebastian Kelm, Jiye Shi, Charlotte M. Deane
MEDELLER: homology-based coordinate generation for membrane proteins. Bioinform. 26 (22) (2010)
Sebastian Kelm, Jiye Shi, Charlotte M. Deane
iMembrane: homology-based membrane-insertion of proteins. Bioinform. 25 (8) (2009)
Waqar Ali, Charlotte M. Deane
Functionally guided alignment of protein interaction networks for module detection. Bioinform. 25 (23) (2009)
Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert
Predicting and Validating Protein Interactions Using Network Structure. PLoS Comput. Biol. 4 (7) (2008)

Charlotte M. Deane.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Charlotte M. Deane