Works by Deane, Charlotte M.

Results: 163

Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure.

Published in:

Bioinformatics, 2000, v. 16, n. 6, p. 513, doi. 10.1093/bioinformatics/16.6.513

By:

Burke, David F.;
Deane, Charlotte M.;
Blundell, Tom L.

Publication type:

Article

KA-Search, a method for rapid and exhaustive sequence identity search of known antibodies.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-38108-7

By:

Olsen, Tobias H.;
Abanades, Brennan;
Moal, Iain H.;
Deane, Charlotte M.

Publication type:

Article

Structurally Mapping Antibody Repertoires.

Published in:

Frontiers in Immunology, 2018, p. N.PAG, doi. 10.3389/fimmu.2018.01698

By:

Krawczyk, Konrad;
Kelm, Sebastian;
Kovaltsuk, Aleksandr;
Galson, Jacob D.;
Kelly, Dominic;
Trück, Johannes;
Regep, Cristian;
Leem, Jinwoo;
Wong, Wing K.;
Nowak, Jaroslaw;
Snowden, James;
Wright, Michael;
Starkie, Laura;
Scott-Tucker, Anthony;
Shi, Jiye;
Deane, Charlotte M.

Publication type:

Article

Discovery and pharmacophoric characterization of chemokine network inhibitors using phage-display, saturation mutagenesis and computational modelling.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41488-z

By:

Vales, Serena;
Kryukova, Jhanna;
Chandra, Soumyanetra;
Smagurauskaite, Gintare;
Payne, Megan;
Clark, Charlie J.;
Hafner, Katrin;
Mburu, Philomena;
Denisov, Stepan;
Davies, Graham;
Outeiral, Carlos;
Deane, Charlotte M.;
Morris, Garrett M.;
Bhattacharya, Shoumo

Publication type:

Article

The imprint of codons on protein structure.

Published in:

Biotechnology Journal, 2011, v. 6, n. 6, p. 641, doi. 10.1002/biot.201000329

By:

Deane, Charlotte M.;
Saunders, Rhodri

Publication type:

Article

Signatures of co-translational folding.

Published in:

Biotechnology Journal, 2011, v. 6, n. 6, p. 742, doi. 10.1002/biot.201000330

By:

Saunders, Rhodri;
Mann, Martin;
Deane, Charlotte M.

Publication type:

Article

Antibody i-Patch prediction of the antibody binding site improves rigid local antibody–antigen docking.

Published in:

PEDS: Protein Engineering, Design & Selection, 2013, v. 26, n. 10, p. 621, doi. 10.1093/protein/gzt043

By:

Krawczyk, Konrad;
Baker, Terry;
Shi, Jiye;
Deane, Charlotte M.

Publication type:

Article

Membranome 3.0: Database of single‐pass membrane proteins with AlphaFold models.

Published in:

Protein Science: A Publication of the Protein Society, 2022, v. 31, n. 5, p. 1, doi. 10.1002/pro.4318

By:

Lomize, Andrei L.;
Schnitzer, Kevin A.;
Todd, Spencer C.;
Cherepanov, Stanislav;
Outeiral, Carlos;
Deane, Charlotte M.;
Pogozheva, Irina D.

Publication type:

Article

Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences.

Published in:

Protein Science: A Publication of the Protein Society, 2022, v. 31, n. 1, p. 141, doi. 10.1002/pro.4205

By:

Olsen, Tobias H.;
Boyles, Fergus;
Deane, Charlotte M.

Publication type:

Article

Measuring rank robustness in scored protein interaction networks.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12859-019-3036-6

By:

Bozhilova, Lyuba V.;
Whitmore, Alan V.;
Wray, Jonny;
Reinert, Gesine;
Deane, Charlotte M.

Publication type:

Article

Progress and challenges in predicting protein interfaces.

Published in:

Briefings in Bioinformatics, 2016, v. 17, n. 1, p. 117, doi. 10.1093/bib/bbv027

By:

Esmaielbeiki, Reyhaneh;
Krawczyk, Konrad;
Knapp, Bernhard;
Nebel, Jean-Christophe;
Deane, Charlotte M.

Publication type:

Article

Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations.

Published in:

Briefings in Bioinformatics, 2015, v. 16, n. 6, p. 1035, doi. 10.1093/bib/bbv005

By:

Knapp, Bernhard;
Demharter, Samuel;
Esmaielbeiki, Reyhaneh;
Deane, Charlotte M.

Publication type:

Article

Different B cell subpopulations show distinct patterns in their IgH repertoire metrics.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.73111

By:

Ghraichy, Marie;
von Niederhäusern, Valentin;
Kovaltsuk, Aleksandr;
Galson, Jacob D.;
Deane, Charlotte M.;
Trück, Johannes

Publication type:

Article

The allosteric modulation of complement C5 by knob domain peptides.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.63586

By:

Macpherson, Alex;
Laabei, Maisem;
Ahdash, Zainab;
Graewert, Melissa A.;
Birtley, James R.;
Schulze, Monika-Sarah E. D.;
Crennell, Susan;
Robinson, Sarah A.;
Holmes, Ben;
Oleinikovas, Vladas;
Nilsson, Per H.;
Snowden, James;
Ellis, Victoria;
Mollnes, Tom Eirik;
Deane, Charlotte M.;
Svergun, Dmitri;
Lawson, Alastair D. G.;
van den Elsen, Jean M. H.

Publication type:

Article

Peptide Centric Vβ Specific Germline Contacts Shape a Specialist T Cell Response.

Published in:

Frontiers in Immunology, 2022, v. 13, p. 1, doi. 10.3389/fimmu.2022.847092

By:

Yang Wang;
Tsitsiklis, Alexandra;
Devoe, Stephanie;
Wei Gao;
Chu, H. Hamlet;
Yan Zhang;
Wei Li;
Wing Ki Wong;
Deane, Charlotte M.;
Neau, David;
Slansky, Jill E.;
Thomas, Paul G.;
Robey, Ellen A.;
Shaodong Dai

Publication type:

Article

The function of communities in protein interaction networks at multiple scales.

Published in:

BMC Systems Biology, 2010, v. 4, p. 100, doi. 10.1186/1752-0509-4-100

By:

Lewis, Anna C. F.;
Jones, Nick S.;
Porter, Mason A.;
Charlotte, Deane M.

Publication type:

Article

Deciphering chemotaxis pathways using cross species comparisons.

Published in:

BMC Systems Biology, 2010, v. 4, p. 3, doi. 10.1186/1752-0509-4-3

By:

Hamer, Rebecca;
Pao-Yang Chen;
Armitage, Judith P.;
Reinert, Gesine;
Deane, Charlotte M.

Publication type:

Article

Using the protein interaction network to predict protein folds without homology.

Published in:

2007

By:

Saeed, Ramazan;
Deane, Charlotte M.

Publication type:

Abstract

A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins.

Published in:

Proteins, 2000, v. 40, n. 1, p. 135, doi. 10.1002/(SICI)1097-0134(20000701)40:1<135::AID-PROT150>3.0.CO;2-1

By:

Deane, Charlotte M.;
Blundell, Tom L.

Publication type:

Article

An iterative structure-assisted approach to sequence alignment and comparative modeling.

Published in:

Proteins, 1999, v. 37, n. S3, p. 55, doi. 10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B

By:

Burke, David F.;
Deane, Charlotte M.;
Nagarajaram, Hampapathalu A.;
Campillo, Nuria;
Martin-Martinez, Mercedes;
Mendes, Joaquim;
Molina, Franck;
Perry, Jeff;
Reddy, B.V.B.;
Soares, Claudio M.;
Steward, Robert E.;
Williams, Mark;
Carrondo, Maria Armenia;
Blundell, Tom L.;
Mizuguchi, Kenji

Publication type:

Article

Structural Bridges through Fold Space.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 9, p. 1, doi. 10.1371/journal.pcbi.1004466

By:

Edwards, Hannah;
Deane, Charlotte M.

Publication type:

Article

Ten Simple Rules for a Successful Cross-Disciplinary Collaboration.

Published in:

2015

By:

Knapp, Bernhard;
Bardenet, Rémi;
Bernabeu, Miguel O.;
Bordas, Rafel;
Bruna, Maria;
Calderhead, Ben;
Cooper, Jonathan;
Fletcher, Alexander G.;
Groen, Derek;
Kuijper, Bram;
Lewis, Joanna;
McInerny, Greg;
Minssen, Timo;
Osborne, James;
Paulitschke, Verena;
Pitt-Francis, Joe;
Todoric, Jelena;
Yates, Christian A.;
Gavaghan, David;
Deane, Charlotte M.

Publication type:

Editorial

Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 9, p. 1, doi. 10.1371/journal.pcbi.1003852

By:

Dunbar, James;
Knapp, Bernhard;
Fuchs, Angelika;
Shi, Jiye;
Deane, Charlotte M.

Publication type:

Article

Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 8, p. 1, doi. 10.1371/journal.pcbi.1003748

By:

Knapp, Bernhard;
Dunbar, James;
Deane, Charlotte M.

Publication type:

Article

Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 11, p. 1, doi. 10.1371/journal.pcbi.1003325

By:

Edwards, Hannah;
Abeln, Sanne;
Deane, Charlotte M.

Publication type:

Article

What Evidence Is There for the Homology of Protein- Protein Interactions?

Published in:

PLoS Computational Biology, 2012, v. 8, n. 9, p. 1, doi. 10.1371/journal.pcbi.1002645

By:

Lewis, Anna C. F.;
Jones, Nick S.;
Porter, Mason A.;
Deane, Charlotte M.

Publication type:

Article

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 6, p. 1, doi. 10.1371/journal.pcbi.1000817

By:

Agarwal, Sumeet;
Deane, Charlotte M.;
Porter, Mason A.;
Jones, Nick S.

Publication type:

Article

Predicting and Validating Protein Interactions Using Network Structure.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 7, p. 1, doi. 10.1371/journal.pcbi.1000118

By:

Pao-Yang Chen;
Deane, Charlotte M.;
Reinert, Gesine

Publication type:

Article

Using Phylogeny to Improve Genome-Wide Distant Homology Recognition.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 1, p. 73, doi. 10.1371/journal.pcbi.0030003

By:

Abeln, Sanne;
Teubner, Carlo;
Deane, Charlotte M.

Publication type:

Article

Prediction of polyspecificity from antibody sequence data by machine learning.

Published in:

Frontiers in Bioinformatics, 2024, p. 1, doi. 10.3389/fbinf.2023.1286883

By:

Éliás, Szabolcs;
Wrzodek, Clemens;
Deane, Charlotte M.;
Tissot, Alain C.;
Klostermann, Stefan;
Ros, Francesca

Publication type:

Article

T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-07708-6

By:

Quast, Nele P.;
Abanades, Brennan;
Guloglu, Bora;
Karuppiah, Vijaykumar;
Harper, Stephen;
Raybould, Matthew I. J.;
Deane, Charlotte M.

Publication type:

Article

Maturation of the Human Immunoglobulin Heavy Chain Repertoire With Age.

Published in:

Frontiers in Immunology, 2020, v. 11, p. N.PAG, doi. 10.3389/fimmu.2020.01734

By:

Ghraichy, Marie;
Galson, Jacob D.;
Kovaltsuk, Aleksandr;
von Niederhäusern, Valentin;
Pachlopnik Schmid, Jana;
Recher, Mike;
Jauch, Annaïse J.;
Miho, Enkelejda;
Kelly, Dominic F.;
Deane, Charlotte M.;
Trück, Johannes

Publication type:

Article

Comparative Analysis of the CDR Loops of Antigen Receptors.

Published in:

Frontiers in Immunology, 2019, p. 1, doi. 10.3389/fimmu.2019.02454

By:

Wong, Wing Ki;
Leem, Jinwoo;
Deane, Charlotte M.

Publication type:

Article

The molecular reach of antibodies crucially underpins their viral neutralisation capacity.

Published in:

Nature Communications, 2025, v. 16, p. 1, doi. 10.1038/s41467-024-54916-5

By:

Huhn, Anna;
Nissley, Daniel;
Wilson, Daniel B.;
Kutuzov, Mikhail A.;
Donat, Robert;
Tan, Tiong Kit;
Zhang, Ying;
Barton, Michael I.;
Liu, Chang;
Dejnirattisai, Wanwisa;
Supasa, Piyada;
Mongkolsapaya, Juthathip;
Townsend, Alain;
James, William;
Screaton, Gavin;
van der Merwe, P. Anton;
Deane, Charlotte M.;
Isaacson, Samuel A.;
Dushek, Omer

Publication type:

Article

Fragmenstein: predicting protein–ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology.

Published in:

Journal of Cheminformatics, 2025, v. 17, n. 1, p. 1, doi. 10.1186/s13321-025-00946-0

By:

Ferla, Matteo P.;
Sánchez-García, Rubén;
Skyner, Rachael E.;
Gahbauer, Stefan;
Taylor, Jenny C.;
von Delft, Frank;
Marsden, Brian D.;
Deane, Charlotte M.

Publication type:

Article

Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures.

Published in:

Journal of Cheminformatics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13321-024-00821-4

By:

Carbery, Anna;
Buttenschoen, Martin;
Skyner, Rachael;
von Delft, Frank;
Deane, Charlotte M.

Publication type:

Article

Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00755-3

By:

Hadfield, Thomas E.;
Scantlebury, Jack;
Deane, Charlotte M.

Publication type:

Article

Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00755-3

By:

Hadfield, Thomas E.;
Scantlebury, Jack;
Deane, Charlotte M.

Publication type:

Article

Examining the Conservation of Kinks in Alpha Helices.

Published in:

PLoS ONE, 2016, v. 11, n. 6, p. 1, doi. 10.1371/journal.pone.0157553

By:

Law, Eleanor C.;
Wilman, Henry R.;
Kelm, Sebastian;
Shi, Jiye;
Deane, Charlotte M.

Publication type:

Article

Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling.

Published in:

Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-023-05744-8

By:

Raybould, Matthew I. J.;
Turnbull, Oliver M.;
Suter, Annabel;
Guloglu, Bora;
Deane, Charlotte M.

Publication type:

Article

ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins.

Published in:

Communications Biology, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42003-023-04927-7

By:

Abanades, Brennan;
Wong, Wing Ki;
Boyles, Fergus;
Georges, Guy;
Bujotzek, Alexander;
Deane, Charlotte M.

Publication type:

Article

The prospects of quantum computing in computational molecular biology.

Published in:

WIREs: Computational Molecular Science, 2021, v. 11, n. 1, p. 1, doi. 10.1002/wcms.1481

By:

Outeiral, Carlos;
Strahm, Martin;
Shi, Jiye;
Morris, Garrett M.;
Benjamin, Simon C.;
Deane, Charlotte M.

Publication type:

Article

Ten simple rules for surviving an interdisciplinary PhD.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 5, p. 1, doi. 10.1371/journal.pcbi.1005512

By:

Demharter, Samuel;
Pearce, Nicholas;
Beattie, Kylie;
Frost, Isabel;
Leem, Jinwoo;
Martin, Alistair;
Oppenheimer, Robert;
Regep, Cristian;
Rukat, Tammo;
Skates, Alexander;
Trendel, Nicola;
Gavaghan, David J.;
Deane, Charlotte M.;
Knapp, Bernhard

Publication type:

Article

Hypergraphs for predicting essential genes using multiprotein complex data.

Published in:

Journal of Complex Networks, 2021, v. 9, n. 2, p. 1, doi. 10.1093/comnet/cnaa028

By:

Klimm, Florian;
Deane, Charlotte M;
Reinert, Gesine

Publication type:

Article

Assessment of model fit via network comparison methods based on subgraph counts.

Published in:

Journal of Complex Networks, 2019, v. 7, n. 2, p. 226, doi. 10.1093/comnet/cny017

By:

Ospina-Forero, Luis;
Deane, Charlotte M;
Reinert, Gesine

Publication type:

Article

Identifying networks with common organizational principles.

Published in:

Journal of Complex Networks, 2018, v. 6, n. 6, p. 887, doi. 10.1093/comnet/cny003

By:

Wegner, Anatol E;
Ospina-Forero, Luis;
Gaunt, Robert E;
Deane, Charlotte M;
Reinert, Gesine

Publication type:

Article

Publisher Correction: The molecular reach of antibodies crucially underpins their viral neutralisation capacity.

Published in:

2025

By:

Huhn, Anna;
Nissley, Daniel;
Wilson, Daniel B.;
Kutuzov, Mikhail A.;
Donat, Robert;
Tan, Tiong Kit;
Zhang, Ying;
Barton, Michael I.;
Liu, Chang;
Dejnirattisai, Wanwisa;
Supasa, Piyada;
Mongkolsapaya, Juthathip;
Townsend, Alain;
James, William;
Screaton, Gavin;
van der Merwe, P. Anton;
Deane, Charlotte M.;
Isaacson, Samuel A.;
Dushek, Omer

Publication type:

Correction Notice

Humatch - fast, gene-specific joint humanisation of antibody heavy and light chains.

Published in:

2024

By:

Chinery, Lewis;
Jeliazkov, Jeliazko R.;
Deane, Charlotte M.

Publication type:

Report

A comparative study of the developability of full-length antibodies, fragments, and bispecific formats reveals higher stability risks for engineered constructs.

Published in:

2024

By:

Condado-Morales, Itzel;
Dingfelder, Fabian;
Waibel, Isabel;
Turnbull, Oliver M.;
Patel, Bhargav;
Cao, Zheng;
Rose Bjelke, Jais;
Nedergaard Grell, Susanne;
Bennet, Anja;
Hummer, Alissa M.;
Raybould, Matthew I. J.;
Deane, Charlotte M.;
Egebjerg, Thomas;
Lorenzen, Nikolai;
Arosio, Paolo

Publication type:

Report

Challenges in antibody structure prediction.

Published in:

mAbs (1942-0862), 2023, v. 15, n. 1, p. 1, doi. 10.1080/19420862.2023.2175319

By:

Fernández-Quintero, Monica L.;
Kokot, Janik;
Waibl, Franz;
Fischer, Anna-Lena M.;
Quoika, Patrick K.;
Deane, Charlotte M.;
Liedl, Klaus R.

Publication type:

Article