Charlotte M. Deane
Orcid: 0000-0003-1388-2252
According to our database1,
Charlotte M. Deane
authored at least 113 papers
between 1998 and 2025.
Collaborative distances:
Collaborative distances:
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Bibliography
2025
Fragmenstein: predicting protein-ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding-based methodology.
J. Cheminformatics, December, 2025
2024
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures.
J. Cheminformatics, December, 2024
The future of machine learning for small-molecule drug discovery will be driven by data.
Nat. Comput. Sci., October, 2024
It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs.
PLoS Comput. Biol., 2024
Nat. Mac. Intell., 2024
Proceedings of the Forty-first International Conference on Machine Learning, 2024
Proceedings of the Forty-first International Conference on Machine Learning, 2024
2023
Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding.
J. Cheminformatics, December, 2023
PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.
J. Chem. Inf. Model., November, 2023
Fragment Merging Using a Graph Database Samples Different Catalogue Space than Similarity Search.
J. Chem. Inf. Model., June, 2023
A Small Step Toward Generalizability: Training a Machine Learning Scoring Function for Structure-Based Virtual Screening.
J. Chem. Inf. Model., May, 2023
Frontiers Bioinform., May, 2023
Testing the limits of SMILES-based de novo molecular generation with curriculum and deep reinforcement learning.
Nat. Mac. Intell., April, 2023
Paragraph - antibody paratope prediction using graph neural networks with minimal feature vectors.
Bioinform., January, 2023
Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions.
Proceedings of the International Conference on Machine Learning, 2023
2022
Generating weighted and thresholded gene coexpression networks using signed distance correlation.
Netw. Sci., 2022
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker.
Nucleic Acids Res., 2022
Incorporating Target-Specific Pharmacophoric Information into Deep Generative Models for Fragment Elaboration.
J. Chem. Inf. Model., 2022
Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained on Docked Poses.
J. Chem. Inf. Model., 2022
Extracting Information from Gene Coexpression Networks of <i>Rhizobium leguminosarum</i>.
J. Comput. Biol., 2022
Bioinform., 2022
Bioinform., 2022
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation.
Bioinform., 2022
Appl. Netw. Sci., 2022
2021
Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies.
PLoS Comput. Biol., 2021
Public Baseline and shared response structures support the theory of antibody repertoire functional commonality.
PLoS Comput. Biol., 2021
J. Complex Networks, 2021
Bioinform., 2021
Bioinform., 2021
Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains.
Bioinform., 2021
Humanization of antibodies using a machine learning approach on large-scale repertoire data.
Bioinform., 2021
2020
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice.
PLoS Comput. Biol., 2020
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., 2020
The evolution of contact prediction: evidence that contact selection in statistical contact prediction is changing.
Bioinform., 2020
Learning from the ligand: using ligand-based features to improve binding affinity prediction.
Bioinform., 2020
2019
PLoS Comput. Biol., 2019
J. Chem. Inf. Model., 2019
HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo.
J. Chem. Inf. Model., 2019
J. Complex Networks, 2019
BMC Bioinform., 2019
Bioinform., 2019
Increasing the accuracy of protein loop structure prediction with evolutionary constraints.
Bioinform., 2019
2018
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., 2018
J. Complex Networks, 2018
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.
Bioinform., 2018
Combining co-evolution and secondary structure prediction to improve fragment library generation.
Bioinform., 2018
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.
Bioinform., 2018
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions.
Bioinform., 2018
2017
Comparing co-evolution methods and their application to template-free protein structure prediction.
Bioinform., 2017
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.
Bioinform., 2017
2016
J. Chem. Inf. Model., 2016
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.
Bioinform., 2016
2015
PLoS Comput. Biol., 2015
J. Comput. Aided Mol. Des., 2015
Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations.
Briefings Bioinform., 2015
2014
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., 2014
Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design.
PLoS Comput. Biol., 2014
J. Chem. Inf. Model., 2014
OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data.
J. Chem. Inf. Model., 2014
J. Comput. Chem., 2014
Improving B-cell epitope prediction and its application to global antibody-antigen docking.
Bioinform., 2014
2013
PLoS Comput. Biol., 2013
Nucleic Acids Res., 2013
Bioinform., 2013
2012
PLoS Comput. Biol., 2012
J. Chem. Inf. Model., 2012
J. Comput. Biol., 2012
Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains.
Adv. Bioinformatics, 2012
2011
Bioinform., 2011
2010
Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks.
PLoS Comput. Biol., 2010
BMC Syst. Biol., 2010
BMC Syst. Biol., 2010
Bioinform., 2010
Bioinform., 2010
2009
Bioinform., 2009
2008
PLoS Comput. Biol., 2008
2007
PLoS Comput. Biol., 2007
BMC Syst. Biol., 2007
A statistical approach using network structure in the prediction of protein characteristics.
Bioinform., 2007
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007
2006
BMC Bioinform., 2006
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006
2005
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005
2001
2000
Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure.
Bioinform., 2000
1998