Charlotte M. Deane

133 papers A* 3Journal 127Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
Assessing the Chemical Intelligence of Large Language Models.
J. Chem. Inf. Model.
Nicholas T. Runcie, Charlotte M. Deane, Fergus Imrie
2025 J jnl
Assessing the Chemical Intelligence of Large Language Models.
CoRR
Nicholas T. Runcie, Charlotte M. Deane, Fergus Imrie
2025 J jnl
Fragmenstein: predicting protein-ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding-based methodology.
J. Cheminformatics
Matteo P. Ferla, Ruben Sanchez-Garcia, Rachael Skyner, Stefan Gahbauer, Jenny C. Taylor, Frank von Delft, Brian D. Marsden, Charlotte M. Deane
2025 J jnl
Investigating the volume and diversity of data needed for generalizable antibody-antigen ΔΔG prediction.
Nat. Comput. Sci.
Alissa M. Hummer, Constantin Schneider, Lewis Chinery, Charlotte M. Deane
2025 J jnl
Kernel-Based Evaluation of Conditional Biological Sequence Models.
CoRR
Pierre Glaser, Steffanie Paul, Alissa M. Hummer, Charlotte M. Deane, Debora S. Marks, Alan Nawzad Amin
2025 J jnl
Mechanistic Interpretability of Antibody Language Models Using SAEs.
CoRR
Rebonto Haque, Oliver M. Turnbull, Anisha Parsan, Nithin Parsan, John J. Yang, Charlotte M. Deane
2025 J jnl
MolSnapper: Conditioning Diffusion for Structure-Based Drug Design.
J. Chem. Inf. Model.
Yael Ziv, Fergus Imrie, Brian D. Marsden, Charlotte M. Deane
2025 J jnl
Robustly interrogating machine learning-based scoring functions: what are they learning?
Bioinform.
Guy Durant, Fergus Boyles, Kristian Birchall, Brian D. Marsden, Charlotte M. Deane
2025 J jnl
STCRpy: a software suite for T-cell receptor structure parsing, interaction profiling, and machine learning dataset preparation.
Bioinform.
Nele P. Quast, Charlotte M. Deane, Matthew I. J. Raybould
2025 J jnl
SigmaDock: Untwisting Molecular Docking With Fragment-Based SE(3) Diffusion.
CoRR
Alvaro Prat, Leo Zhang, Charlotte M. Deane, Yee Whye Teh, Garrett M. Morris
2025 J jnl
Transformers trained on proteins can learn to attend to Euclidean distance.
CoRR
Isaac Ellmen, Constantin Schneider, Matthew I. J. Raybould, Charlotte M. Deane
2025 J jnl
Transformers trained on proteins can learn to attend to Euclidean distance.
Trans. Mach. Learn. Res.
Isaac Ellmen, Constantin Schneider, Matthew I. J. Raybould, Charlotte M. Deane
2024 J jnl
ABodyBuilder3: Improved and scalable antibody structure predictions.
CoRR
Henry Kenlay, Frédéric A. Dreyer, Daniel Cutting, Daniel A. Nissley, Charlotte M. Deane
2024 J jnl
ABodyBuilder3: improved and scalable antibody structure predictions.
Bioinform.
Henry Kenlay, Frédéric A. Dreyer, Daniel Cutting, Daniel A. Nissley, Charlotte M. Deane
2024 J jnl
Addressing the antibody germline bias and its effect on language models for improved antibody design.
Bioinform.
Tobias Hegelund Olsen, Iain H. Moal, Charlotte M. Deane
2024 J jnl
Codon language embeddings provide strong signals for use in protein engineering.
Nat. Mac. Intell.
Carlos Outeiral, Charlotte M. Deane
2024 A* conf
Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design.
ICML
Leo Klarner, Tim G. J. Rudner, Garrett M. Morris, Charlotte M. Deane, Yee Whye Teh
2024 J jnl
Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design.
CoRR
Leo Klarner, Tim G. J. Rudner, Garrett M. Morris, Charlotte M. Deane, Yee Whye Teh
2024 J jnl
De novo antibody design with SE(3) diffusion.
CoRR
Daniel Cutting, Frédéric A. Dreyer, David Errington, Constantin Schneider, Charlotte M. Deane
2024 J jnl
It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs.
PLoS Comput. Biol.
Yang Jiang, Charlotte M. Deane, Garrett M. Morris, Edward P. O'Brien
2024 A* conf
Kernel-Based Evaluation of Conditional Biological Sequence Models.
ICML
Pierre Glaser, Steffanie Paul, Alissa M. Hummer, Charlotte M. Deane, Debora Susan Marks, Alan Nawzad Amin
2024 J jnl
Large scale paired antibody language models.
CoRR
Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane
2024 J jnl
Large scale paired antibody language models.
PLoS Comput. Biol.
Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane
2024 J jnl
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures.
J. Cheminformatics
Anna Carbery, Martin Buttenschoen, Rachael Skyner, Frank von Delft, Charlotte M. Deane
2024 J jnl
The future of machine learning for small-molecule drug discovery will be driven by data.
Nat. Comput. Sci.
Guy Durant, Fergus Boyles, Kristian Birchall, Charlotte M. Deane
2024 J jnl
Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking.
Bioinform.
Marco Giulini, Constantin Schneider, Daniel Cutting, Nikita Desai, Charlotte M. Deane, Alexandre M. J. J. Bonvin
2024 J jnl
p-IgGen: a paired antibody generative language model.
Bioinform.
Oliver M. Turnbull, Dino Oglic, Rebecca Croasdale-Wood, Charlotte M. Deane
2023 J jnl
A Small Step Toward Generalizability: Training a Machine Learning Scoring Function for Structure-Based Virtual Screening.
J. Chem. Inf. Model.
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
2023 A* conf
Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions.
ICML
Leo Klarner, Tim G. J. Rudner, Michael Reutlinger, Torsten Schindler, Garrett M. Morris, Charlotte M. Deane, Yee Whye Teh
2023 J jnl
Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions.
CoRR
Leo Klarner, Tim G. J. Rudner, Michael Reutlinger, Torsten Schindler, Garrett M. Morris, Charlotte M. Deane, Yee Whye Teh
2023 J jnl
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding.
J. Cheminformatics
Thomas E. Hadfield, Jack Scantlebury, Charlotte M. Deane
2023 J jnl
Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search.
J. Chem. Inf. Model.
Stephanie Wills, Ruben Sanchez-Garcia, Tim Dudgeon, Stephen D. Roughley, Andy Merritt, Roderick E. Hubbard, James Davidson, Frank von Delft, Charlotte M. Deane
2023 J jnl
Inverse folding for antibody sequence design using deep learning.
CoRR
Frédéric A. Dreyer, Daniel Cutting, Constantin Schneider, Henry Kenlay, Charlotte M. Deane
2023 J jnl
PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.
J. Chem. Inf. Model.
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
2023 J jnl
Paragraph - antibody paratope prediction using graph neural networks with minimal feature vectors.
Bioinform.
Lewis Chinery, Newton Wahome, Iain H. Moal, Charlotte M. Deane
2023 J jnl
Prediction of polyspecificity from antibody sequence data by machine learning.
Frontiers Bioinform.
Szabolcs Elias, Clemens Wrzodek, Charlotte M. Deane, Alain C. Tissot, Stefan Klostermann, Francesca Ros
2023 J jnl
Testing the limits of SMILES-based de novo molecular generation with curriculum and deep reinforcement learning.
Nat. Mac. Intell.
Maranga Mokaya, Fergus Imrie, Willem P. van Hoorn, Aleksandra Kalisz, Anthony R. Bradley, Charlotte M. Deane
2022 J jnl
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation.
Bioinform.
Brennan Abanades, Guy Georges, Alexander Bujotzek, Charlotte M. Deane
2022 J jnl
Current structure predictors are not learning the physics of protein folding.
Bioinform.
Carlos Outeiral, Daniel A. Nissley, Charlotte M. Deane
2022 J jnl
DLAB: deep learning methods for structure-based virtual screening of antibodies.
Bioinform.
Constantin Schneider, Andrew Buchanan, Bruck Taddese, Charlotte M. Deane
2022 J jnl
Extracting Information from Gene Coexpression Networks of
J. Comput. Biol.
Javier Pardo-Diaz, Mariano Beguerisse-Díaz, Philip S. Poole, Charlotte M. Deane, Gesine Reinert
2022 J jnl
Generating weighted and thresholded gene coexpression networks using signed distance correlation.
Netw. Sci.
Javier Pardo-Diaz, Philip S. Poole, Mariano Beguerisse-Díaz, Charlotte M. Deane, Gesine Reinert
2022 J jnl
Incorporating Target-Specific Pharmacophoric Information into Deep Generative Models for Fragment Elaboration.
J. Chem. Inf. Model.
Thomas E. Hadfield, Fergus Imrie, Andy Merritt, Kristian Birchall, Charlotte M. Deane
2022 J jnl
Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained on Docked Poses.
J. Chem. Inf. Model.
Fergus Boyles, Charlotte M. Deane, Garrett M. Morris
2022 J jnl
Ranking of Communities in Multiplex Spatiotemporal Models of Brain Dynamics.
CoRR
James B. Wilsenach, Catherine E. Warnaby, Charlotte M. Deane, Gesine D. Reinert
2022 J jnl
Ranking of communities in multiplex spatiotemporal models of brain dynamics.
Appl. Netw. Sci.
James B. Wilsenach, Catherine E. Warnaby, Charlotte M. Deane, Gesine Reinert
2022 J jnl
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker.
Nucleic Acids Res.
Constantin Schneider, Matthew I. J. Raybould, Charlotte M. Deane
2021 J jnl
COGENT: evaluating the consistency of gene co-expression networks.
Bioinform.
Lyuba V. Bozhilova, Javier Pardo-Diaz, Gesine Reinert, Charlotte M. Deane
2021 J jnl
Co-evolutionary distance predictions contain flexibility information.
Bioinform.
Dominik Schwarz, Guy Georges, Sebastian Kelm, Jiye Shi, Anna Vangone, Charlotte M. Deane
2021 J jnl
CoV-AbDab: the coronavirus antibody database.
Bioinform.
Matthew I. J. Raybould, Aleksandr Kovaltsuk, Claire Marks, Charlotte M. Deane
2021 J jnl
Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies.
PLoS Comput. Biol.
Sarah A. Robinson, Matthew I. J. Raybould, Constantin Schneider, Wing Ki Wong, Claire Marks, Charlotte M. Deane
2021 J jnl
Generating property-matched decoy molecules using deep learning.
Bioinform.
Fergus Imrie, Anthony R. Bradley, Charlotte M. Deane
2021 J jnl
Humanization of antibodies using a machine learning approach on large-scale repertoire data.
Bioinform.
Claire Marks, Alissa M. Hummer, Mark Chin, Charlotte M. Deane
2021 J jnl
Hypergraphs for predicting essential genes using multiprotein complex data.
J. Complex Networks
Florian Klimm, Charlotte M. Deane, Gesine Reinert
2021 J jnl
Public Baseline and shared response structures support the theory of antibody repertoire functional commonality.
PLoS Comput. Biol.
Matthew I. J. Raybould, Claire Marks, Aleksandr Kovaltsuk, Alan P. Lewis, Jiye Shi, Charlotte M. Deane
2021 J jnl
Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains.
Bioinform.
Daniel A. Nissley, Anna Carbery, Mark Chonofsky, Charlotte M. Deane
2021 J jnl
Robust gene coexpression networks using signed distance correlation.
Bioinform.
Javier Pardo-Diaz, Lyuba V. Bozhilova, Mariano Beguerisse-Díaz, Philip S. Poole, Charlotte M. Deane, Gesine Reinert
2020 J jnl
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.
Jack Scantlebury, Nathan Brown, Frank von Delft, Charlotte M. Deane
2020 J jnl
Deep Generative Models for 3D Linker Design.
J. Chem. Inf. Model.
Fergus Imrie, Anthony R. Bradley, Mihaela van der Schaar, Charlotte M. Deane
2020 J jnl
Learning from the ligand: using ligand-based features to improve binding affinity prediction.
Bioinform.
Fergus Boyles, Charlotte M. Deane, Garrett M. Morris
2020 J jnl
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice.
PLoS Comput. Biol.
Aleksandr Kovaltsuk, Matthew I. J. Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück, Charlotte M. Deane
2020 J jnl
TCRBuilder: multi-state T-cell receptor structure prediction.
Bioinform.
Wing Ki Wong, Claire Marks, Jinwoo Leem, Alan P. Lewis, Jiye Shi, Charlotte M. Deane
2020 J jnl
The evolution of contact prediction: evidence that contact selection in statistical contact prediction is changing.
Bioinform.
Mark Chonofsky, Saulo Henrique Pires de Oliveira, Konrad Krawczyk, Charlotte M. Deane
2020 J jnl
Thera-SAbDab: the Therapeutic Structural Antibody Database.
Nucleic Acids Res.
Matthew I. J. Raybould, Claire Marks, Alan P. Lewis, Jiye Shi, Alexander Bujotzek, Bruck Taddese, Charlotte M. Deane
2019 J jnl
Assessment of model fit via network comparison methods based on subgraph counts.
J. Complex Networks
Luis Ospina-Forero, Charlotte M. Deane, Gesine Reinert
2019 J jnl
HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo.
J. Chem. Inf. Model.
Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary
2019 J jnl
Increasing the accuracy of protein loop structure prediction with evolutionary constraints.
Bioinform.
Claire Marks, Charlotte M. Deane
2019 J jnl
Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening.
J. Chem. Inf. Model.
Jean-Paul Ebejer, Paul W. Finn, Wing Ki Wong, Charlotte M. Deane, Garrett M. Morris
2019 J jnl
MHC binding affects the dynamics of different T-cell receptors in different ways.
PLoS Comput. Biol.
Bernhard Knapp, P. Anton van der Merwe, Omer Dushek, Charlotte M. Deane
2019 J jnl
Measuring rank robustness in scored protein interaction networks.
BMC Bioinform.
Lyuba V. Bozhilova, Alan Whitmore, Jonny Wray, Gesine Reinert, Charlotte M. Deane
2019 J jnl
SCALOP: sequence-based antibody canonical loop structure annotation.
Bioinform.
Wing Ki Wong, Guy Georges, Francesca Ros, Sebastian Kelm, Alan P. Lewis, Bruck Taddese, Jinwoo Leem, Charlotte M. Deane
2018 J jnl
Combining co-evolution and secondary structure prediction to improve fragment library generation.
Bioinform.
Saulo Henrique Pires de Oliveira, Charlotte M. Deane
2018 J jnl
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.
Bioinform.
Malte Lücken, M. J. T. Page, A. J. Crosby, S. Mason, Gesine Reinert, Charlotte M. Deane
2018 J jnl
Identifying networks with common organizational principles.
J. Complex Networks
Anatol E. Wegner, Luis Ospina-Forero, Robert E. Gaunt, Charlotte M. Deane, Gesine Reinert
2018 J jnl
In silico structural modeling of multiple epigenetic marks on DNA.
Bioinform.
Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary
2018 J jnl
Predicting loop conformational ensembles.
Bioinform.
Claire Marks, Jiye Shi, Charlotte M. Deane
2018 J jnl
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.
Fergus Imrie, Anthony R. Bradley, Mihaela van der Schaar, Charlotte M. Deane
2018 J jnl
STCRDab: the structural T-cell receptor database.
Nucleic Acids Res.
Jinwoo Leem, Saulo Henrique Pires de Oliveira, Konrad Krawczyk, Charlotte M. Deane
2018 J jnl
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.
Bioinform.
Saulo Henrique Pires de Oliveira, Eleanor C. Law, Jiye Shi, Charlotte M. Deane
2018 J jnl
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions.
Bioinform.
Bernhard Knapp, Marta Alcalá, Hao Zhang, Clare E. West, P. Anton van der Merwe, Charlotte M. Deane
2017 J jnl
Comparing co-evolution methods and their application to template-free protein structure prediction.
Bioinform.
Saulo Henrique Pires de Oliveira, Jiye Shi, Charlotte M. Deane
2017 J jnl
Identifying networks with common organizational principles.
CoRR
Anatol E. Wegner, Luis Ospina-Forero, Robert E. Gaunt, Charlotte M. Deane, Gesine Reinert
2017 J jnl
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.
Bioinform.
Claire Marks, Jaroslaw Nowak, Stefan Klostermann, Guy Georges, James Dunbar, Jiye Shi, Sebastian Kelm, Charlotte M. Deane
2017 J jnl
Ten simple rules for surviving an interdisciplinary PhD.
PLoS Comput. Biol.
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
2016 J jnl
ANARCI: antigen receptor numbering and receptor classification.
Bioinform.
James Dunbar, Charlotte M. Deane
2016 J jnl
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.
Bioinform.
Bernhard Knapp, Samuel Demharter, Charlotte M. Deane, Peter Minary
2016 J jnl
Progress and challenges in predicting protein interfaces.
Briefings Bioinform.
Reyhaneh Esmaielbeiki, Konrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane
2016 J jnl
SAbPred: a structure-based antibody prediction server.
Nucleic Acids Res.
James Dunbar, Konrad Krawczyk, Jinwoo Leem, Claire Marks, Jaroslaw Nowak, Cristian Regep, Guy Georges, Sebastian Kelm, Bojana Popovic, Charlotte M. Deane
2016 J jnl
T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex.
J. Chem. Inf. Model.
Bernhard Knapp, Charlotte M. Deane
2016 J jnl
Tertiary Element Interaction in HIV-1 TAR.
J. Chem. Inf. Model.
Konrad Krawczyk, Adelene Y. L. Sim, Bernhard Knapp, Charlotte M. Deane, Peter Minary
2015 J jnl
Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations.
Briefings Bioinform.
Bernhard Knapp, Samuel Demharter, Reyhaneh Esmaielbeiki, Charlotte M. Deane
2015 J jnl
Structural Bridges through Fold Space.
PLoS Comput. Biol.
Hannah Edwards, Charlotte M. Deane
2015 J jnl
Ten Simple Rules for a Successful Cross-Disciplinary Collaboration.
PLoS Comput. Biol.
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
2015 J jnl
WONKA: objective novel complex analysis for ensembles of protein-ligand structures.
J. Comput. Aided Mol. Des.
Anthony R. Bradley, Ian D. Wall, Frank von Delft, Darren V. S. Green, Charlotte M. Deane, Brian D. Marsden
2014 J jnl
Alignment-free protein interaction network comparison.
Bioinform.
Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane
2014 J jnl
Crowdsourcing Yields a New Standard for Kinks in Protein Helices.
J. Chem. Inf. Model.
Henry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, Bernhard Knapp
2014 J jnl
Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design.
PLoS Comput. Biol.
James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M. Deane
2014 J jnl
Gro2mat: A package to efficiently read gromacs output in MATLAB.
J. Comput. Chem.
Hung Dien, Charlotte M. Deane, Bernhard Knapp
2014 J jnl
Improving B-cell epitope prediction and its application to global antibody-antigen docking.
Bioinform.
Konrad Krawczyk, Xiaofeng Liu, Terry Baker, Jiye Shi, Charlotte M. Deane
2014 J jnl
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.
Bernhard Knapp, James Dunbar, Charlotte M. Deane
2014 J jnl
OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data.
J. Chem. Inf. Model.
Anthony R. Bradley, Ian D. Wall, Darren V. S. Green, Charlotte M. Deane, Brian D. Marsden
2014 J jnl
SAbDab: the structural antibody database.
Nucleic Acids Res.
James Dunbar, Konrad Krawczyk, Jinwoo Leem, Terry Baker, Angelika Fuchs, Guy Georges, Jiye Shi, Charlotte M. Deane
2014 J jnl
Ten Simple Rules for Effective Computational Research.
PLoS Comput. Biol.
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
2013 J jnl
Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies.
PLoS Comput. Biol.
Hannah Edwards, Sanne Abeln, Charlotte M. Deane
2013 J jnl
MP-T: improving membrane protein alignment for structure prediction.
Bioinform.
Jamie R. Hill, Charlotte M. Deane
2013 J jnl
Memoir: template-based structure prediction for membrane proteins.
Nucleic Acids Res.
Jean-Paul Ebejer, Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
2012 J jnl
Freely Available Conformer Generation Methods: How Good Are They?
J. Chem. Inf. Model.
Jean-Paul Ebejer, Garrett M. Morris, Charlotte M. Deane
2012 J jnl
Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains.
Adv. Bioinformatics
Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte M. Deane
2012 J jnl
The Importance of Age and High Degree, in Protein-Protein Interaction Networks.
J. Comput. Biol.
Tiago Rito, Charlotte M. Deane, Gesine Reinert
2012 J jnl
What Evidence Is There for the Homology of Protein-Protein Interactions?
PLoS Comput. Biol.
Anna C. F. Lewis, Nick S. Jones, Mason A. Porter, Charlotte M. Deane
2011 J jnl
Environment specific substitution tables improve membrane protein alignment.
Bioinform.
Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
2010 J jnl
Deciphering chemotaxis pathways using cross species comparisons.
BMC Syst. Biol.
Rebecca Hamer, Pao-Yang Chen, Judith P. Armitage, Gesine Reinert, Charlotte M. Deane
2010 J jnl
Directionality in protein fold prediction.
BMC Bioinform.
Jonathan J. Ellis, Fabien P. E. Huard, Charlotte M. Deane, Sheenal Srivastava, Graham R. Wood
2010 J jnl
Exploring the potential of template-based modelling.
Bioinform.
Braddon K. Lance, Charlotte M. Deane, Graham R. Wood
2010 J jnl
How threshold behaviour affects the use of subgraphs for network comparison.
Bioinform.
Tiago Rito, Zi Wang, Charlotte M. Deane, Gesine Reinert
2010 J jnl
MEDELLER: homology-based coordinate generation for membrane proteins.
Bioinform.
Sebastian Kelm, Jiye Shi, Charlotte M. Deane
2010 J jnl
Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks.
PLoS Comput. Biol.
Sumeet Agarwal, Charlotte M. Deane, Mason A. Porter, Nick S. Jones
2010 J jnl
The function of communities in protein interaction networks at multiple scales.
BMC Syst. Biol.
Anna C. F. Lewis, Nick S. Jones, Mason A. Porter, Charlotte M. Deane
2009 J jnl
Functionally guided alignment of protein interaction networks for module detection.
Bioinform.
Waqar Ali, Charlotte M. Deane
2009 J jnl
iMembrane: homology-based membrane-insertion of proteins.
Bioinform.
Sebastian Kelm, Jiye Shi, Charlotte M. Deane
2008 J jnl
An assessment of the uses of homologous interactions.
Bioinform.
Ramazan Saeed, Charlotte M. Deane
2008 J jnl
Predicting and Validating Protein Interactions Using Network Structure.
PLoS Comput. Biol.
Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert
2007 J jnl
A statistical approach using network structure in the prediction of protein characteristics.
Bioinform.
Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert
2007 — conf
Cotranslational protein folding - fact or fiction?
ISMB/ECCB (Supplement of Bioinformatics)
Charlotte M. Deane, Mingqiang Dong, Fabien P. E. Huard, Braddon K. Lance, Graham R. Wood
2007 J jnl
Linking evolution of protein structures through fragments.
BMC Syst. Biol.
Sanne Abeln, Charlotte M. Deane
2007 J jnl
Using Phylogeny to Improve Genome-Wide Distant Homology Recognition.
PLoS Comput. Biol.
Sanne Abeln, Carlo Teubner, Charlotte M. Deane
2007 J jnl
Using the protein interaction network to predict protein folds without homology.
BMC Syst. Biol.
Ramazan Saeed, Charlotte M. Deane
2006 — conf
Modelling sequential protein folding under kinetic control.
ISMB (Supplement of Bioinformatics)
Fabien P. E. Huard, Charlotte M. Deane, Graham R. Wood
2006 J jnl
Protein protein interactions, evolutionary rate, abundance and age.
BMC Bioinform.
Ramazan Saeed, Charlotte M. Deane
2005 — conf
How old is your fold?
ISMB (Supplement of Bioinformatics)
Henry F. Winstanley, Sanne Abeln, Charlotte M. Deane
2001 J jnl
SCORE: predicting the core of protein models.
Bioinform.
Charlotte M. Deane, Quentin Kaas, Tom L. Blundell
2000 J jnl
Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure.
Bioinform.
David F. Burke, Charlotte M. Deane, Tom L. Blundell
1998 J jnl
JOY: protein sequence-structure representation and analysis.
Bioinform.
Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington