Assessing the Chemical Intelligence of Large Language Models.

Charlotte M. Deane https://scholar.google.com/citations?user=QAdcBnQAAAAJ https://mathgenealogy.org/id.php?id=162922 https://en.wikipedia.org/wiki/Charlotte_Deane https://orcid.org/0000-0003-1388-2252 https://www.wikidata.org/entity/Q41048456

Nicholas T. Runcie Charlotte M. Deane Fergus Imrie Assessing the Chemical Intelligence of Large Language Models. 216-227 2026 66 J. Chem. Inf. Model. 1 https://doi.org/10.1021/acs.jcim.5c02145 db/journals/jcisd/jcisd66.html#RuncieDI26 streams/journals/jcisd

Guy Durant Fergus Boyles Kristian Birchall Brian D. Marsden Charlotte M. Deane Robustly interrogating machine learning-based scoring functions: what are they learning? 2025 41 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btaf040 db/journals/bioinformatics/bioinformatics41.html#DurantBBMD25

Nele P. Quast Charlotte M. Deane Matthew I. J. Raybould STCRpy: a software suite for T-cell receptor structure parsing, interaction profiling, and machine learning dataset preparation. 2025 41 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btaf566 db/journals/bioinformatics/bioinformatics41.html#QuastDR25 streams/journals/bioinformatics

Daniel Cutting Frédéric A. Dreyer David Errington Constantin Schneider Charlotte M. Deane <i>De Novo</i> Antibody Design with SE(3) Diffusion. 351-361 2025 32 J. Comput. Biol. 4 https://doi.org/10.1089/cmb.2024.0768 db/journals/jcb/jcb32.html#CuttingDESD25 streams/journals/jcb

Matteo P. Ferla Ruben Sanchez-Garcia Rachael Skyner Stefan Gahbauer Jenny C. Taylor Frank von Delft Brian D. Marsden Charlotte M. Deane Fragmenstein: predicting protein-ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding-based methodology. 4 2025 December 17 J. Cheminformatics 1 https://doi.org/10.1186/s13321-025-00946-0 db/journals/jcheminf/jcheminf17.html#FerlaSSGTDMD25 streams/journals/jcheminf

Yael Ziv Fergus Imrie Brian D. Marsden Charlotte M. Deane MolSnapper: Conditioning Diffusion for Structure-Based Drug Design. 4263-4273 2025 65 J. Chem. Inf. Model. 9 https://doi.org/10.1021/acs.jcim.4c02008 db/journals/jcisd/jcisd65.html#ZivIMD25 streams/journals/jcisd

Alissa M. Hummer Constantin Schneider Lewis Chinery Charlotte M. Deane Investigating the volume and diversity of data needed for generalizable antibody-antigen ΔΔG prediction. 635-647 2025 August 5 Nat. Comput. Sci. 8 https://doi.org/10.1038/s43588-025-00823-8 db/journals/ncs/ncs5.html#HummerSCD25 streams/journals/ncs

Isaac Ellmen Constantin Schneider Matthew I. J. Raybould Charlotte M. Deane Transformers trained on proteins can learn to attend to Euclidean distance. 2025 2025 Trans. Mach. Learn. Res. https://openreview.net/forum?id=mU59bDyqqv db/journals/tmlr/tmlr2025.html#EllmenSRD25 streams/journals/tmlr

Isaac Ellmen Constantin Schneider Matthew I. J. Raybould Charlotte M. Deane Transformers trained on proteins can learn to attend to Euclidean distance. 2025 February abs/2502.01533 CoRR https://doi.org/10.48550/arXiv.2502.01533 db/journals/corr/corr2502.html#abs-2502-01533 streams/journals/corr

Nicholas T. Runcie Charlotte M. Deane Fergus Imrie Assessing the Chemical Intelligence of Large Language Models. 2025 May abs/2505.07735 CoRR https://doi.org/10.48550/arXiv.2505.07735 db/journals/corr/corr2505.html#abs-2505-07735 streams/journals/corr

Pierre Glaser Steffanie Paul Alissa M. Hummer Charlotte M. Deane Debora S. Marks Alan Nawzad Amin Kernel-Based Evaluation of Conditional Biological Sequence Models. 2025 October abs/2510.15601 CoRR https://doi.org/10.48550/arXiv.2510.15601 db/journals/corr/corr2510.html#abs-2510-15601 streams/journals/corr

Alvaro Prat Leo Zhang Charlotte M. Deane Yee Whye Teh Garrett M. Morris SigmaDock: Untwisting Molecular Docking With Fragment-Based SE(3) Diffusion. 2025 November abs/2511.04854 CoRR https://doi.org/10.48550/arXiv.2511.04854 db/journals/corr/corr2511.html#abs-2511-04854 streams/journals/corr

Rebonto Haque Oliver M. Turnbull Anisha Parsan Nithin Parsan John J. Yang Charlotte M. Deane Mechanistic Interpretability of Antibody Language Models Using SAEs. 2025 December abs/2512.05794 CoRR https://doi.org/10.48550/arXiv.2512.05794 db/journals/corr/corr2512.html#abs-2512-05794 streams/journals/corr

Marco Giulini Constantin Schneider Daniel Cutting Nikita Desai Charlotte M. Deane Alexandre M. J. J. Bonvin Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking. 2024 40 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btae583 db/journals/bioinformatics/bioinformatics40.html#GiuliniSCDDB24

Henry Kenlay Frédéric A. Dreyer Daniel Cutting Daniel A. Nissley Charlotte M. Deane ABodyBuilder3: improved and scalable antibody structure predictions. 2024 40 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btae576 db/journals/bioinformatics/bioinformatics40.html#KenlayDCND24

Tobias Hegelund Olsen Iain H. Moal Charlotte M. Deane Addressing the antibody germline bias and its effect on language models for improved antibody design. 2024 40 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btae618 db/journals/bioinformatics/bioinformatics40.html#OlsenMD24

Oliver M. Turnbull Dino Oglic Rebecca Croasdale-Wood Charlotte M. Deane p-IgGen: a paired antibody generative language model. 2024 40 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btae659 db/journals/bioinformatics/bioinformatics40.html#TurnbullOCD24

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. 32 2024 December 16 J. Cheminformatics 1 https://doi.org/10.1186/s13321-024-00821-4 https://www.wikidata.org/entity/Q130691691 db/journals/jcheminf/jcheminf16.html#CarberyBSDD24

Carlos Outeiral Charlotte M. Deane Codon language embeddings provide strong signals for use in protein engineering. 170-179 2024 6 Nat. Mac. Intell. 2 https://doi.org/10.1038/s42256-024-00791-0 https://www.wikidata.org/entity/Q130683198 db/journals/natmi/natmi6.html#OuteiralD24 streams/journals/natmi

Guy Durant Fergus Boyles Kristian Birchall Charlotte M. Deane The future of machine learning for small-molecule drug discovery will be driven by data. 735-743 2024 October 4 Nat. Comput. Sci. 10 https://doi.org/10.1038/s43588-024-00699-0 db/journals/ncs/ncs4.html#DurantBBD24 streams/journals/ncs

Yang Jiang 0004 Charlotte M. Deane Garrett M. Morris Edward P. O'Brien It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs. 1011901 2024 20 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1011901 https://www.wikidata.org/entity/Q128152820 db/journals/ploscb/ploscb20.html#JiangDMO24 streams/journals/ploscb

Henry Kenlay Frédéric A. Dreyer Aleksandr Kovaltsuk Dom Miketa Douglas Pires Charlotte M. Deane Large scale paired antibody language models. 1012646 2024 20 PLoS Comput. Biol. 12 https://doi.org/10.1371/journal.pcbi.1012646 db/journals/ploscb/ploscb20.html#KenlayDKMPD24 streams/journals/ploscb

Pierre Glaser Steffanie Paul Alissa M. Hummer Charlotte M. Deane Debora Susan Marks Alan Nawzad Amin Kernel-Based Evaluation of Conditional Biological Sequence Models. 2024 ICML https://proceedings.mlr.press/v235/glaser24a.html https://openreview.net/forum?id=2dlmcTXfcY conf/icml/2024 db/conf/icml/icml2024.html#GlaserPHDMA24 15678-15705 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. 2024 ICML https://proceedings.mlr.press/v235/klarner24a.html https://openreview.net/forum?id=8NfHmzo0Op conf/icml/2024 db/conf/icml/icml2024.html#KlarnerRMDT24 24770-24807

Henry Kenlay Frédéric A. Dreyer Aleksandr Kovaltsuk Dom Miketa Douglas Pires Charlotte M. Deane Large scale paired antibody language models. 2024 abs/2403.17889 CoRR https://doi.org/10.48550/arXiv.2403.17889 db/journals/corr/corr2403.html#abs-2403-17889

Daniel Cutting Frédéric A. Dreyer David Errington Constantin Schneider Charlotte M. Deane De novo antibody design with SE(3) diffusion. 2024 abs/2405.07622 CoRR https://doi.org/10.48550/arXiv.2405.07622 db/journals/corr/corr2405.html#abs-2405-07622

Henry Kenlay Frédéric A. Dreyer Daniel Cutting Daniel A. Nissley Charlotte M. Deane ABodyBuilder3: Improved and scalable antibody structure predictions. 2024 abs/2405.20863 CoRR https://doi.org/10.48550/arXiv.2405.20863 db/journals/corr/corr2405.html#abs-2405-20863

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. 2024 abs/2407.11942 CoRR https://doi.org/10.48550/arXiv.2407.11942 db/journals/corr/corr2407.html#abs-2407-11942 streams/journals/corr

Lewis Chinery Newton Wahome Iain H. Moal Charlotte M. Deane Paragraph - antibody paratope prediction using graph neural networks with minimal feature vectors. 2023 January 39 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btac732 db/journals/bioinformatics/bioinformatics39.html#ChineryWMD23

Szabolcs Elias Clemens Wrzodek Charlotte M. Deane Alain C. Tissot Stefan Klostermann Francesca Ros Prediction of polyspecificity from antibody sequence data by machine learning. 2023 May 3 Frontiers Bioinform. https://doi.org/10.3389/fbinf.2023.1286883 db/journals/fbinf/fbinf3.html#EliasWDTKR23

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. 84 2023 December 15 J. Cheminformatics 1 https://doi.org/10.1186/s13321-023-00755-3 db/journals/jcheminf/jcheminf15.html#HadfieldSD23

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. 2960-2974 2023 May 63 J. Chem. Inf. Model. 10 https://doi.org/10.1021/acs.jcim.3c00322 db/journals/jcisd/jcisd63.html#ScantleburyVCHTBCDGDD23

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. 3423-3437 2023 June 63 J. Chem. Inf. Model. 11 https://doi.org/10.1021/acs.jcim.3c00276 db/journals/jcisd/jcisd63.html#WillsSDRMHDDD23

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. 6964-6971 2023 November 63 J. Chem. Inf. Model. 22 https://doi.org/10.1021/acs.jcim.3c01490 db/journals/jcisd/jcisd63.html#HoerschingerWPLDGKFL23

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. 386-394 2023 April 5 Nat. Mac. Intell. 4 https://doi.org/10.1038/s42256-023-00636-2 db/journals/natmi/natmi5.html#MokayaIHKBD23

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. 17176-17197 2023 ICML https://proceedings.mlr.press/v202/klarner23a.html conf/icml/2023 db/conf/icml/icml2023.html#KlarnerRRSMDT23

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. 2023 abs/2307.15073 CoRR https://doi.org/10.48550/arXiv.2307.15073 db/journals/corr/corr2307.html#abs-2307-15073

Frédéric A. Dreyer Daniel Cutting Constantin Schneider Henry Kenlay Charlotte M. Deane Inverse folding for antibody sequence design using deep learning. 2023 abs/2310.19513 CoRR https://doi.org/10.48550/arXiv.2310.19513 db/journals/corr/corr2310.html#abs-2310-19513

James B. Wilsenach Catherine E. Warnaby Charlotte M. Deane Gesine Reinert Ranking of communities in multiplex spatiotemporal models of brain dynamics. 15 2022 7 Appl. Netw. Sci. 1 https://doi.org/10.1007/s41109-022-00454-2 db/journals/ans/ans7.html#WilsenachWDR22

Constantin Schneider Andrew Buchanan Bruck Taddese Charlotte M. Deane DLAB: deep learning methods for structure-based virtual screening of antibodies. 377-383 2022 38 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btab660 db/journals/bioinformatics/bioinformatics38.html#SchneiderBTD22

Brennan Abanades Guy Georges Alexander Bujotzek Charlotte M. Deane ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation. 1877-1880 2022 38 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btac016 db/journals/bioinformatics/bioinformatics38.html#AbanadesGBD22

Carlos Outeiral Daniel A. Nissley Charlotte M. Deane Current structure predictors are not learning the physics of protein folding. 1881-1887 2022 38 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btab881 db/journals/bioinformatics/bioinformatics38.html#OuteiralND22

Javier Pardo-Diaz Mariano Beguerisse-Díaz Philip S. Poole Charlotte M. Deane Gesine Reinert Extracting Information from Gene Coexpression Networks of <i>Rhizobium leguminosarum</i>. 752-768 2022 29 J. Comput. Biol. 7 https://doi.org/10.1089/cmb.2021.0600 db/journals/jcb/jcb29.html#Pardo-DiazBPDR22

Thomas E. Hadfield Fergus Imrie Andy Merritt Kristian Birchall Charlotte M. Deane Incorporating Target-Specific Pharmacophoric Information into Deep Generative Models for Fragment Elaboration. 2280-2292 2022 62 J. Chem. Inf. Model. 10 https://doi.org/10.1021/acs.jcim.1c01311 https://www.wikidata.org/entity/Q112565036 db/journals/jcisd/jcisd62.html#HadfieldIMBD22

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. 5329-5341 2022 62 J. Chem. Inf. Model. 22 https://doi.org/10.1021/acs.jcim.1c00096 db/journals/jcisd/jcisd62.html#BoylesDM22

Constantin Schneider Matthew I. J. Raybould Charlotte M. Deane SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker. 1368-1372 2022 50 Nucleic Acids Res. D1 https://doi.org/10.1093/nar/gkab1050 https://www.wikidata.org/entity/Q112682445 db/journals/nar/nar50.html#SchneiderRD22

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. 131-145 2022 10 Netw. Sci. 2 https://doi.org/10.1017/nws.2022.13 db/journals/netsci/netsci10.html#Pardo-DiazPBDR22

Matthew I. J. Raybould Daniel A. Nissley Sandeep Kumar Charlotte M. Deane Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies. 2022 July https://doi.org/10.5281/zenodo.6862376 Zenodo streams/repo/zenodo data/11/RaybouldNKD22b Matthew I. J. Raybould Daniel A. Nissley Sandeep Kumar Charlotte M. Deane Computationally profiling peptide:MHC recognition by T-cell receptors and T-cell receptor-mimetic antibodies. 2022 July https://doi.org/10.5281/zenodo.7220531 Zenodo streams/repo/zenodo data/11/RaybouldNKD22b

James B. Wilsenach Catherine E. Warnaby Charlotte M. Deane Gesine D. Reinert Ranking of Communities in Multiplex Spatiotemporal Models of Brain Dynamics. 2022 abs/2203.09281 CoRR https://doi.org/10.48550/arXiv.2203.09281 db/journals/corr/corr2203.html#abs-2203-09281

Matthew I. J. Raybould Aleksandr Kovaltsuk Claire Marks Charlotte M. Deane CoV-AbDab: the coronavirus antibody database. 734-735 2021 37 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btaa739 https://www.wikidata.org/entity/Q98508364 db/journals/bioinformatics/bioinformatics37.html#RaybouldKMD21

Daniel A. Nissley Anna Carbery Mark Chonofsky Charlotte M. Deane Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains. 1853-1859 2021 37 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btab020 db/journals/bioinformatics/bioinformatics37.html#NissleyCCD21

Lyuba V. Bozhilova Javier Pardo-Diaz Gesine Reinert Charlotte M. Deane COGENT: evaluating the consistency of gene co-expression networks. 1928-1929 2021 37 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btaa787 db/journals/bioinformatics/bioinformatics37.html#BozhilovaPRD21

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. 1982-1989 2021 37 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btab041 db/journals/bioinformatics/bioinformatics37.html#Pardo-DiazBBPDR21

Fergus Imrie Anthony R. Bradley Charlotte M. Deane Generating property-matched decoy molecules using deep learning. 2134-2141 2021 37 Bioinform. 15 https://doi.org/10.1093/bioinformatics/btab080 db/journals/bioinformatics/bioinformatics37.html#ImrieBD21

Claire Marks Alissa M. Hummer Mark Chin Charlotte M. Deane Humanization of antibodies using a machine learning approach on large-scale repertoire data. 4041-4047 2021 37 Bioinform. 22 https://doi.org/10.1093/bioinformatics/btab434 db/journals/bioinformatics/bioinformatics37.html#MarksHCD21

Dominik Schwarz Guy Georges Sebastian Kelm Jiye Shi Anna Vangone Charlotte M. Deane Co-evolutionary distance predictions contain flexibility information. 65-72 2021 38 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btab562 db/journals/bioinformatics/bioinformatics38.html#SchwarzGKSVD21

Florian Klimm Charlotte M. Deane Gesine Reinert Hypergraphs for predicting essential genes using multiprotein complex data. 2021 9 J. Complex Networks 2 https://doi.org/10.1093/comnet/cnaa028 db/journals/compnet/compnet9.html#KlimmDR21

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. 2021 17 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1008781 db/journals/ploscb/ploscb17.html#RaybouldMKLSD21

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. 2021 17 PLoS Comput. Biol. 12 https://doi.org/10.1371/journal.pcbi.1009675 https://www.wikidata.org/entity/Q112574051 db/journals/ploscb/ploscb17.html#RobinsonRSWMD21

Fergus Boyles Charlotte M. Deane Garrett M. Morris Learning from the ligand: using ligand-based features to improve binding affinity prediction. 758-764 2020 36 Bioinform. 3 https://doi.org/10.1093/bioinformatics/btz665 https://www.wikidata.org/entity/Q90621725 db/journals/bioinformatics/bioinformatics36.html#BoylesDM20

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. 1750-1756 2020 36 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btz816 https://www.wikidata.org/entity/Q91142121 db/journals/bioinformatics/bioinformatics36.html#ChonofskyOKD20

Wing Ki Wong Claire Marks Jinwoo Leem Alan P. Lewis Jiye Shi Charlotte M. Deane TCRBuilder: multi-state T-cell receptor structure prediction. 3580-3581 2020 36 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btaa194 https://www.wikidata.org/entity/Q90387817 db/journals/bioinformatics/bioinformatics36.html#WongMLLSD20

Fergus Imrie Anthony R. Bradley Mihaela van der Schaar Charlotte M. Deane Deep Generative Models for 3D Linker Design. 1983-1995 2020 60 J. Chem. Inf. Model. 4 https://doi.org/10.1021/acs.jcim.9b01120 https://www.wikidata.org/entity/Q90488930 db/journals/jcisd/jcisd60.html#ImrieBSD20

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. 3722-3730 2020 60 J. Chem. Inf. Model. 8 https://doi.org/10.1021/acs.jcim.0c00263 https://www.wikidata.org/entity/Q97676950 db/journals/jcisd/jcisd60.html#ScantleburyBDD20

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. D383-D388 2020 48 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkz827 https://www.wikidata.org/entity/Q90294900 db/journals/nar/nar48.html#RaybouldMLSBTD20

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. 2020 16 PLoS Comput. Biol. 2 https://doi.org/10.1371/journal.pcbi.1007636 https://www.wikidata.org/entity/Q89759205 db/journals/ploscb/ploscb16.html#KovaltsukRWMKST20

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. 1774-1776 2019 35 Bioinform. 10 https://doi.org/10.1093/bioinformatics/bty877 https://www.wikidata.org/entity/Q57461421 db/journals/bioinformatics/bioinformatics35.html#WongGRKLTLD19

Claire Marks Charlotte M. Deane Increasing the accuracy of protein loop structure prediction with evolutionary constraints. 2585-2592 2019 35 Bioinform. 15 https://doi.org/10.1093/bioinformatics/bty996 https://www.wikidata.org/entity/Q90392112 db/journals/bioinformatics/bioinformatics35.html#MarksD19

Lyuba V. Bozhilova Alan Whitmore Jonny Wray Gesine Reinert Charlotte M. Deane Measuring rank robustness in scored protein interaction networks. 446:1-446:14 2019 20 BMC Bioinform. 1 https://doi.org/10.1186/s12859-019-3036-6 https://www.wikidata.org/entity/Q92962253 db/journals/bmcbi/bmcbi20.html#BozhilovaWWRD19

Luis Ospina-Forero Charlotte M. Deane Gesine Reinert Assessment of model fit via network comparison methods based on subgraph counts. 226-253 2019 7 J. Complex Networks 2 https://doi.org/10.1093/comnet/cny017 db/journals/compnet/compnet7.html#Ospina-ForeroDR19

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. 2600-2616 2019 59 J. Chem. Inf. Model. 6 https://doi.org/10.1021/acs.jcim.8b00779 https://www.wikidata.org/entity/Q92221080 db/journals/jcisd/jcisd59.html#EbejerFWDM19

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. 2894-2899 2019 59 J. Chem. Inf. Model. 6 https://doi.org/10.1021/acs.jcim.9b00104 https://www.wikidata.org/entity/Q91881150 db/journals/jcisd/jcisd59.html#DemharterKDM19

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. 2019 15 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1007338 https://www.wikidata.org/entity/Q93196269 db/journals/ploscb/ploscb15.html#KnappMDD19

Konrad Krawczyk Samuel Demharter Bernhard Knapp Charlotte M. Deane Peter Minary In silico structural modeling of multiple epigenetic marks on DNA. 41-48 2018 34 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btx516 https://www.wikidata.org/entity/Q47801260 db/journals/bioinformatics/bioinformatics34.html#KrawczykDKDM18

Claire Marks Jiye Shi Charlotte M. Deane Predicting loop conformational ensembles. 949-956 2018 34 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btx718 https://www.wikidata.org/entity/Q47307363 db/journals/bioinformatics/bioinformatics34.html#MarksSD18

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. 994-1000 2018 34 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btx706 https://www.wikidata.org/entity/Q47308929 db/journals/bioinformatics/bioinformatics34.html#LuckenPCMRD18

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. 1132-1140 2018 34 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btx722 https://www.wikidata.org/entity/Q47307343 db/journals/bioinformatics/bioinformatics34.html#OliveiraLSD18

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. 1941-1943 2018 34 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btx842 https://www.wikidata.org/entity/Q50063150 db/journals/bioinformatics/bioinformatics34.html#KnappAZWMD18

Saulo Henrique Pires de Oliveira Charlotte M. Deane Combining co-evolution and secondary structure prediction to improve fragment library generation. 2219-2227 2018 34 Bioinform. 13 https://doi.org/10.1093/bioinformatics/bty084 https://www.wikidata.org/entity/Q57979372 db/journals/bioinformatics/bioinformatics34.html#OliveiraD18

Anatol E. Wegner Luis Ospina-Forero Robert E. Gaunt Charlotte M. Deane Gesine Reinert Identifying networks with common organizational principles. 887-913 2018 6 J. Complex Networks 6 https://doi.org/10.1093/comnet/cny003 https://www.wikidata.org/entity/Q57979370 db/journals/compnet/compnet6.html#WegnerOGDR18

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. 2319-2330 2018 58 J. Chem. Inf. Model. 11 https://doi.org/10.1021/acs.jcim.8b00350 https://www.wikidata.org/entity/Q57056976 db/journals/jcisd/jcisd58.html#ImrieBSD18

Jinwoo Leem Saulo Henrique Pires de Oliveira Konrad Krawczyk Charlotte M. Deane STCRDab: the structural T-cell receptor database. D406-D412 2018 46 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkx971 https://www.wikidata.org/entity/Q47102975 db/journals/nar/nar46.html#LeemOKD18

Saulo Henrique Pires de Oliveira Jiye Shi Charlotte M. Deane Comparing co-evolution methods and their application to template-free protein structure prediction. 373-381 2017 33 Bioinform. 3 https://doi.org/10.1093/bioinformatics/btw618 https://www.wikidata.org/entity/Q38974044 db/journals/bioinformatics/bioinformatics33.html#OliveiraSD17

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. 1346-1353 2017 33 Bioinform. 9 https://doi.org/10.1093/bioinformatics/btw823 https://www.wikidata.org/entity/Q38814529 db/journals/bioinformatics/bioinformatics33.html#MarksNKGDSKD17

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. 2017 13 PLoS Comput. Biol. 5 https://doi.org/10.1371/journal.pcbi.1005512 https://www.wikidata.org/entity/Q42346453 db/journals/ploscb/ploscb13.html#DemharterPBFLMO17

Anatol E. Wegner Luis Ospina-Forero Robert E. Gaunt Charlotte M. Deane Gesine Reinert Identifying networks with common organizational principles. 2017 abs/1704.00387 CoRR http://arxiv.org/abs/1704.00387 db/journals/corr/corr1704.html#WegnerOGDR17

Reyhaneh Esmaielbeiki Konrad Krawczyk Bernhard Knapp Jean-Christophe Nebel Charlotte M. Deane Progress and challenges in predicting protein interfaces. 117-131 2016 17 Briefings Bioinform. 1 https://doi.org/10.1093/bib/bbv027 https://www.wikidata.org/entity/Q28602320 db/journals/bib/bib17.html#EsmaielbeikiKKN16

Bernhard Knapp Samuel Demharter Charlotte M. Deane Peter Minary Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo. 181-186 2016 32 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btv502 https://www.wikidata.org/entity/Q40512928 db/journals/bioinformatics/bioinformatics32.html#KnappDDM16

James Dunbar Charlotte M. Deane ANARCI: antigen receptor numbering and receptor classification. 298-300 2016 32 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btv552 https://www.wikidata.org/entity/Q30379792 db/journals/bioinformatics/bioinformatics32.html#DunbarD16

Bernhard Knapp Charlotte M. Deane T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex. 46-53 2016 56 J. Chem. Inf. Model. 1 https://doi.org/10.1021/acs.jcim.5b00511 https://www.wikidata.org/entity/Q40245378 db/journals/jcisd/jcisd56.html#KnappD16

Konrad Krawczyk Adelene Y. L. Sim Bernhard Knapp Charlotte M. Deane Peter Minary Tertiary Element Interaction in HIV-1 TAR. 1746-1754 2016 56 J. Chem. Inf. Model. 9 https://doi.org/10.1021/acs.jcim.6b00152 https://www.wikidata.org/entity/Q40631464 db/journals/jcisd/jcisd56.html#KrawczykSKDM16

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. W474-W478 2016 44 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkw361 https://www.wikidata.org/entity/Q41723956 db/journals/nar/nar44.html#DunbarKLMNRGKPD16

Bernhard Knapp Samuel Demharter Reyhaneh Esmaielbeiki Charlotte M. Deane Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations. 1035-1044 2015 16 Briefings Bioinform. 6 https://doi.org/10.1093/bib/bbv005 https://www.wikidata.org/entity/Q38366025 db/journals/bib/bib16.html#KnappDED15

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. 963-973 2015 29 J. Comput. Aided Mol. Des. 10 https://doi.org/10.1007/s10822-015-9866-z https://www.wikidata.org/entity/Q40521899 db/journals/jcamd/jcamd29.html#BradleyWDGDM15

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. 2015 11 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1004214 https://www.wikidata.org/entity/Q28974680 db/journals/ploscb/ploscb11.html#KnappBBBBCCFGKL15

Hannah Edwards Charlotte M. Deane Structural Bridges through Fold Space. 2015 11 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1004466 https://www.wikidata.org/entity/Q27317945 db/journals/ploscb/ploscb11.html#EdwardsD15

Konrad Krawczyk Xiaofeng Liu Terry Baker Jiye Shi Charlotte M. Deane Improving B-cell epitope prediction and its application to global antibody-antigen docking. 2288-2294 2014 30 Bioinform. 16 https://doi.org/10.1093/bioinformatics/btu190 https://www.wikidata.org/entity/Q42005239 db/journals/bioinformatics/bioinformatics30.html#KrawczykLBSD14

Waqar Ali Tiago Rito Gesine Reinert Fengzhu Sun Charlotte M. Deane Alignment-free protein interaction network comparison. 430-437 2014 30 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btu447 https://www.wikidata.org/entity/Q34103155 db/journals/bioinformatics/bioinformatics30.html#AliRRSD14

Hung Dien Charlotte M. Deane Bernhard Knapp Gro2mat: A package to efficiently read gromacs output in MATLAB. 1528-1531 2014 35 J. Comput. Chem. 20 https://doi.org/10.1002/jcc.23650 https://www.wikidata.org/entity/Q51080024 db/journals/jcc/jcc35.html#DienDK14

Henry R. Wilman Jean-Paul Ebejer Jiye Shi Charlotte M. Deane Bernhard Knapp Crowdsourcing Yields a New Standard for Kinks in Protein Helices. 2585-2593 2014 54 J. Chem. Inf. Model. 9 https://doi.org/10.1021/ci500403a https://www.wikidata.org/entity/Q45949703 db/journals/jcisd/jcisd54.html#WilmanESDK14

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. 2636-2646 2014 54 J. Chem. Inf. Model. 10 https://doi.org/10.1021/ci500245d https://www.wikidata.org/entity/Q30854428 db/journals/jcisd/jcisd54.html#BradleyWGDM14

James Dunbar Konrad Krawczyk Jinwoo Leem Terry Baker Angelika Fuchs Guy Georges Jiye Shi Charlotte M. Deane SAbDab: the structural antibody database. 1140-1146 2014 42 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkt1043 https://www.wikidata.org/entity/Q38494687 db/journals/nar/nar42.html#DunbarKLBFGSD14

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 0001 Christian A. Yates David Gavaghan Stephen Emmott Charlotte M. Deane Ten Simple Rules for Effective Computational Research. 2014 10 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1003506 https://www.wikidata.org/entity/Q28974696 db/journals/ploscb/ploscb10.html#OsborneBBCCDDFFGKMMPSWYGED14

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. 2014 10 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1003748 https://www.wikidata.org/entity/Q24288783 db/journals/ploscb/ploscb10.html#KnappDD14a

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. 2014 10 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1003852 https://www.wikidata.org/entity/Q35262045 db/journals/ploscb/ploscb10.html#DunbarKFSD14

Jamie R. Hill Charlotte M. Deane MP-T: improving membrane protein alignment for structure prediction. 54-61 2013 29 Bioinform. 1 https://doi.org/10.1093/bioinformatics/bts640 https://www.wikidata.org/entity/Q44731767 db/journals/bioinformatics/bioinformatics29.html#HillD13

Jean-Paul Ebejer Jamie R. Hill Sebastian Kelm Jiye Shi Charlotte M. Deane Memoir: template-based structure prediction for membrane proteins. 379-383 2013 41 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkt331 https://www.wikidata.org/entity/Q30155100 db/journals/nar/nar41.html#EbejerHKSD13

Hannah Edwards Sanne Abeln Charlotte M. Deane Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies. 2013 9 PLoS Comput. Biol. 11 https://doi.org/10.1371/journal.pcbi.1003325 https://www.wikidata.org/entity/Q34038948 db/journals/ploscb/ploscb9.html#EdwardsAD13

Martin Mann Rhodri Saunders Cameron Smith Rolf Backofen Charlotte M. Deane Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains. 2012 2012 Adv. Bioinformatics https://doi.org/10.1155/2012/148045 https://www.wikidata.org/entity/Q30420785 db/journals/abi/abi2012.html#MannSSBD12 148045:1-148045:6

Tiago Rito Charlotte M. Deane Gesine Reinert The Importance of Age and High Degree, in Protein-Protein Interaction Networks. 785-795 2012 19 J. Comput. Biol. 6 https://doi.org/10.1089/cmb.2012.0054 https://www.wikidata.org/entity/Q47623802 db/journals/jcb/jcb19.html#RitoDR12

Jean-Paul Ebejer Garrett M. Morris Charlotte M. Deane Freely Available Conformer Generation Methods: How Good Are They? 1146-1158 2012 52 J. Chem. Inf. Model. 5 https://doi.org/10.1021/ci2004658 https://www.wikidata.org/entity/Q51386173 db/journals/jcisd/jcisd52.html#EbejerMD12

Anna C. F. Lewis Nick S. Jones Mason A. Porter Charlotte M. Deane What Evidence Is There for the Homology of Protein-Protein Interactions? 2012 8 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1002645 https://www.wikidata.org/entity/Q34426308 db/journals/ploscb/ploscb8.html#LewisJPD12

Jamie R. Hill Sebastian Kelm Jiye Shi Charlotte M. Deane Environment specific substitution tables improve membrane protein alignment. 15-23 2011 27 Bioinform. 13 https://doi.org/10.1093/bioinformatics/btr230 https://www.wikidata.org/entity/Q42762248 db/journals/bioinformatics/bioinformatics27.html#HillKSD11

Braddon K. Lance Charlotte M. Deane Graham R. Wood Exploring the potential of template-based modelling. 1849-1856 2010 26 Bioinform. 15 https://doi.org/10.1093/bioinformatics/btq294 https://www.wikidata.org/entity/Q48205333 db/journals/bioinformatics/bioinformatics26.html#LanceDW10

Tiago Rito Zi Wang Charlotte M. Deane Gesine Reinert How threshold behaviour affects the use of subgraphs for network comparison. 2010 26 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btq386 https://www.wikidata.org/entity/Q41955932 db/journals/bioinformatics/bioinformatics26.html#RitoWDR10

Sebastian Kelm Jiye Shi Charlotte M. Deane MEDELLER: homology-based coordinate generation for membrane proteins. 2833-2840 2010 26 Bioinform. 22 https://doi.org/10.1093/bioinformatics/btq554 https://www.wikidata.org/entity/Q33711713 db/journals/bioinformatics/bioinformatics26.html#KelmSD10

Jonathan J. Ellis Fabien P. E. Huard Charlotte M. Deane Sheenal Srivastava Graham R. Wood Directionality in protein fold prediction. 172 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-172 https://www.wikidata.org/entity/Q30387760 db/journals/bmcbi/bmcbi11.html#EllisHDSW10

Rebecca Hamer Pao-Yang Chen Judith P. Armitage Gesine Reinert Charlotte M. Deane Deciphering chemotaxis pathways using cross species comparisons. 3 2010 4 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-4-3 https://www.wikidata.org/entity/Q33523188 db/journals/bmcsb/bmcsb4.html#HamerCARD10

Anna C. F. Lewis Nick S. Jones Mason A. Porter Charlotte M. Deane The function of communities in protein interaction networks at multiple scales. 100 2010 4 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-4-100 https://www.wikidata.org/entity/Q30986238 db/journals/bmcsb/bmcsb4.html#LewisJPD10

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. 2010 6 PLoS Comput. Biol. 6 https://doi.org/10.1371/journal.pcbi.1000817 https://www.wikidata.org/entity/Q33619022 db/journals/ploscb/ploscb6.html#AgarwalDPJ10

Sebastian Kelm Jiye Shi Charlotte M. Deane iMembrane: homology-based membrane-insertion of proteins. 1086-1088 2009 25 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btp102 https://www.wikidata.org/entity/Q30375116 db/journals/bioinformatics/bioinformatics25.html#KelmSD09

Waqar Ali Charlotte M. Deane Functionally guided alignment of protein interaction networks for module detection. 3166-3173 2009 25 Bioinform. 23 https://doi.org/10.1093/bioinformatics/btp569 https://www.wikidata.org/entity/Q41814236 db/journals/bioinformatics/bioinformatics25.html#AliD09

Ramazan Saeed Charlotte M. Deane An assessment of the uses of homologous interactions. 689-695 2008 24 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btm576 https://www.wikidata.org/entity/Q48373262 db/journals/bioinformatics/bioinformatics24.html#SaeedD08

Pao-Yang Chen Charlotte M. Deane Gesine Reinert Predicting and Validating Protein Interactions Using Network Structure. 2008 4 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1000118 https://www.wikidata.org/entity/Q33354928 db/journals/ploscb/ploscb4.html#ChenDR08

Pao-Yang Chen Charlotte M. Deane Gesine Reinert A statistical approach using network structure in the prediction of protein characteristics. 2314-2321 2007 23 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btm342 https://www.wikidata.org/entity/Q48395044 db/journals/bioinformatics/bioinformatics23.html#ChenDR07

Ramazan Saeed Charlotte M. Deane Using the protein interaction network to predict protein folds without homology. P69 2007 1 BMC Syst. Biol. S-1 https://doi.org/10.1186/1752-0509-1-S1-P69 db/journals/bmcsb/bmcsb1S.html#SaeedD07

Sanne Abeln Charlotte M. Deane Linking evolution of protein structures through fragments. S12 2007 1 BMC Syst. Biol. S-1 https://doi.org/10.1186/1752-0509-1-S1-S12 https://www.wikidata.org/entity/Q57951391 db/journals/bmcsb/bmcsb1S.html#AbelnD07

Sanne Abeln Carlo Teubner Charlotte M. Deane Using Phylogeny to Improve Genome-Wide Distant Homology Recognition. 2007 3 PLoS Comput. Biol. 1 https://doi.org/10.1371/journal.pcbi.0030003 https://www.wikidata.org/entity/Q33269791 db/journals/ploscb/ploscb3.html#AbelnTD07

Charlotte M. Deane Mingqiang Dong Fabien P. E. Huard Braddon K. Lance Graham R. Wood Cotranslational protein folding - fact or fiction? 142-148 2007 conf/ismb/2007 ISMB/ECCB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/btm175 https://www.wikidata.org/entity/Q30363004 db/conf/ismb/ismb2007.html#DeaneDHLW07

Ramazan Saeed Charlotte M. Deane Protein protein interactions, evolutionary rate, abundance and age. 128 2006 7 BMC Bioinform. https://doi.org/10.1186/1471-2105-7-128 https://www.wikidata.org/entity/Q33236253 db/journals/bmcbi/bmcbi7.html#SaeedD06

Fabien P. E. Huard Charlotte M. Deane Graham R. Wood Modelling sequential protein folding under kinetic control. 203-210 2006 conf/ismb/2006 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/btl248 https://www.wikidata.org/entity/Q48437539 db/conf/ismb/ismb2006.html#HuardDW06 Henry F. Winstanley Sanne Abeln Charlotte M. Deane How old is your fold? 449-458 2005 conf/ismb/2005 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/bti1008 https://www.wikidata.org/entity/Q30350894 db/conf/ismb/ismb2005.html#WinstanleyAD05

Charlotte M. Deane Quentin Kaas Tom L. Blundell SCORE: predicting the core of protein models. 541-550 2001 17 Bioinform. 6 db/journals/bioinformatics/bioinformatics17.html#DeaneKB01 https://doi.org/10.1093/bioinformatics/17.6.541 https://www.wikidata.org/entity/Q48561281

David F. Burke Charlotte M. Deane Tom L. Blundell Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure. 513-519 2000 16 Bioinform. 6 db/journals/bioinformatics/bioinformatics16.html#BurkeDB00 https://doi.org/10.1093/bioinformatics/16.6.513 https://www.wikidata.org/entity/Q48562841

Kenji Mizuguchi Charlotte M. Deane Tom L. Blundell Mark S. Johnson John P. Overington JOY: protein sequence-structure representation and analysis. 617-623 1998 14 Bioinform. 7 db/journals/bioinformatics/bioinformatics14.html#MizuguchiDBJO98 https://doi.org/10.1093/bioinformatics/14.7.617 https://www.wikidata.org/entity/Q30431389

Brennan Abanades Sanne Abeln Sumeet Agarwal Marta Alcalá Waqar Ali Alan Nawzad Amin Judith P. Armitage Rolf Backofen Terry Baker Rémi Bardenet Kylie Beattie Mariano Beguerisse-Díaz Miguel O. Bernabeu Kristian Birchall Tom L. Blundell Alexandre M. J. J. Bonvin Rafel Bordas Fergus Boyles Lyuba V. Bozhilova Anthony R. Bradley Nathan Brown Maria Bruna Andrew Buchanan Alexander Bujotzek David F. Burke Martin Buttenschoen Ben Calderhead Anna Carbery Pao-Yang Chen Vijil Chenthamarakshan Mark Chin Lewis Chinery Mark Chonofsky Jonathan Cooper Rebecca Croasdale-Wood A. J. Crosby Daniel Cutting Neil Dalchau Payel Das James Davidson Frank von Delft Samuel Demharter Nikita Desai Hung Dien Mingqiang Dong Frédéric A. Dreyer Tim Dudgeon James Dunbar Sara-Jane Dunn Guy Durant Omer Dushek Jean-Paul Ebejer Hannah Edwards Szabolcs Elias Jonathan J. Ellis Isaac Ellmen Stephen Emmott David Errington Reyhaneh Esmaielbeiki Matteo P. Ferla Monica L. Fernández-Quintero Paul W. Finn Alexander G. Fletcher Robin Freeman Isabel Frost Angelika Fuchs Stefan Gahbauer Robert E. Gaunt David GavaghanDavid J. Gavaghan Guy Georges Marco Giulini Pierre Glaser Darren V. S. Green Derek Groen Harold Grosjean Thomas E. Hadfield Rebecca Hamer Rebonto Haque Jamie R. Hill Valentin J. Hoerschinger Willem P. van Hoorn Fabien P. E. Huard Roderick E. Hubbard Alissa M. Hummer Fergus Imrie Yang Jiang 0004 Mark S. Johnson Nick S. Jones Quentin Kaas Aleksandra Kalisz Sebastian Kelm Henry Kenlay Hubert Kettenberger Leo Klarner Florian Klimm Stefan Klostermann Bernhard Knapp Aleksandr Kovaltsuk Konrad Krawczyk Bram Kuijper Sandeep Kumar Braddon K. Lance Eleanor C. Law Jinwoo Leem Alan P. Lewis Anna C. F. Lewis Joanna Lewis Klaus R. Liedl Xiaofeng Liu Johannes R. Loeffler Malte Lücken Claire Marks Debora S. MarksDebora Susan Marks Brian D. Marsden Alistair Martin S. Mason Greg J. McInerny Andy Merritt P. Anton van der Merwe Dom Miketa Peter Minary Timo Minssen Gary R. Mirams Kenji Mizuguchi Iain H. Moal Maranga Mokaya Garrett M. Morris Jean-Christophe Nebel Daniel A. Nissley Jaroslaw Nowak Edward P. O'Brien Dino Oglic Saulo Henrique Pires de Oliveira Tobias Hegelund Olsen Robert Oppenheimer James M. Osborne Luis Ospina-Forero Carlos Outeiral John P. Overington M. J. T. Page Javier Pardo-Diaz Anisha Parsan Nithin Parsan Steffanie Paul Verena Paulitschke Nicholas Pearce Douglas E. V. PiresDouglas Pires Joe Pitt-Francis Nancy D. Pomarici Philip S. Poole Bojana Popovic Mason A. Porter Alvaro Prat Nele QuastNele P. Quast Martin RadenMartin Mann Matthew I. J. Raybould Cristian Regep Gesine ReinertGesine D. Reinert Michael Reutlinger Tiago Rito Sarah A. Robinson Francesca Ros Stephen D. Roughley Tim G. J. Rudner Tammo Rukat Nicholas T. Runcie Ramazan Saeed Ruben Sanchez-Garcia Rhodri Saunders Jack Scantlebury Mihaela van der Schaar Torsten Schindler Constantin Schneider Dominik Schwarz Biswa Sengupta Jiye Shi Adelene Y. L. Sim Alexander Skates Rachael Skyner Cameron Smith James Snowden Sheenal Srivastava Fengzhu Sun Bruck Taddese Jenny C. Taylor Yee Whye Teh Carlo Teubner Alain C. Tissot Jelena Todoric Nicola Trendel Johannes Trück Oliver M. Turnbull Anna Vangone Lucy Vost Newton Wahome Franz Waibl Ian D. Wall Zi Wang Catherine E. Warnaby Anatol E. Wegner Clare E. West Alan Whitmore Stephanie Wills Henry R. Wilman James B. Wilsenach Henry F. Winstanley Wing Ki Wong Graham R. Wood Jonny Wray David W. Wright 0001 Clemens Wrzodek John J. Yang Christian A. Yates Hao Zhang Leo Zhang Yael Ziv