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Looking for therapeutic antibodies in next-generation sequencing repositories.

Krawczyk K, Raybould MIJ, Kovaltsuk A, Deane CM.

MAbs. 2019 Jul 17:1-9. doi: 10.1080/19420862.2019.1633884. [Epub ahead of print]


Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening.

Ebejer JP, Finn PW, Wong WK, Deane CM, Morris GM.

J Chem Inf Model. 2019 Jun 24;59(6):2600-2616. doi: 10.1021/acs.jcim.8b00779. Epub 2019 Jun 4.


Five computational developability guidelines for therapeutic antibody profiling.

Raybould MIJ, Marks C, Krawczyk K, Taddese B, Nowak J, Lewis AP, Bujotzek A, Shi J, Deane CM.

Proc Natl Acad Sci U S A. 2019 Feb 14. pii: 201810576. doi: 10.1073/pnas.1810576116. [Epub ahead of print]


Increasing the accuracy of protein loop structure prediction with evolutionary constraints.

Marks C, Deane CM.

Bioinformatics. 2019 Aug 1;35(15):2585-2592. doi: 10.1093/bioinformatics/bty996.


Filtering Next-Generation Sequencing of the Ig Gene Repertoire Data Using Antibody Structural Information.

Kovaltsuk A, Krawczyk K, Kelm S, Snowden J, Deane CM.

J Immunol. 2018 Dec 15;201(12):3694-3704. doi: 10.4049/jimmunol.1800669. Epub 2018 Nov 5.


Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas.

Knapp B, Ospina L, Deane CM.

J Chem Theory Comput. 2018 Dec 11;14(12):6127-6138. doi: 10.1021/acs.jctc.8b00391. Epub 2018 Nov 9.


SCALOP: sequence-based antibody canonical loop structure annotation.

Wong WK, Georges G, Ros F, Kelm S, Lewis AP, Taddese B, Leem J, Deane CM.

Bioinformatics. 2019 May 15;35(10):1774-1776. doi: 10.1093/bioinformatics/bty877.


High-Throughput Antibody Structure Modeling and Design Using ABodyBuilder.

Leem J, Deane CM.

Methods Mol Biol. 2019;1851:367-380. doi: 10.1007/978-1-4939-8736-8_21.


Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data.

Imrie F, Bradley AR, van der Schaar M, Deane CM.

J Chem Inf Model. 2018 Nov 26;58(11):2319-2330. doi: 10.1021/acs.jcim.8b00350. Epub 2018 Oct 16.


Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires.

Kovaltsuk A, Leem J, Kelm S, Snowden J, Deane CM, Krawczyk K.

J Immunol. 2018 Oct 15;201(8):2502-2509. doi: 10.4049/jimmunol.1800708. Epub 2018 Sep 14.


Structurally Mapping Antibody Repertoires.

Krawczyk K, Kelm S, Kovaltsuk A, Galson JD, Kelly D, Trück J, Regep C, Leem J, Wong WK, Nowak J, Snowden J, Wright M, Starkie L, Scott-Tucker A, Shi J, Deane CM.

Front Immunol. 2018 Jul 23;9:1698. doi: 10.3389/fimmu.2018.01698. eCollection 2018.


A statistical model for helices with applications.

Mardia KV, Sriram K, Deane CM.

Biometrics. 2018 Sep;74(3):845-854. doi: 10.1111/biom.12870. Epub 2018 Mar 22.


Combining co-evolution and secondary structure prediction to improve fragment library generation.

de Oliveira SHP, Deane CM.

Bioinformatics. 2018 Jul 1;34(13):2219-2227. doi: 10.1093/bioinformatics/bty084.


pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions.

Knapp B, Alcala M, Zhang H, West CE, van der Merwe PA, Deane CM.

Bioinformatics. 2018 Jun 1;34(11):1941-1943. doi: 10.1093/bioinformatics/btx842.


Antibody side chain conformations are position-dependent.

Leem J, Georges G, Shi J, Deane CM.

Proteins. 2018 Apr;86(4):383-392. doi: 10.1002/prot.25453. Epub 2018 Jan 25. Erratum in: Proteins. 2018 Aug;86(8):892.


How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data.

Kovaltsuk A, Krawczyk K, Galson JD, Kelly DF, Deane CM, Trück J.

Front Immunol. 2017 Dec 8;8:1753. doi: 10.3389/fimmu.2017.01753. eCollection 2017. Review.


Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.

de Oliveira SHP, Law EC, Shi J, Deane CM.

Bioinformatics. 2018 Apr 1;34(7):1132-1140. doi: 10.1093/bioinformatics/btx722.


Predicting loop conformational ensembles.

Marks C, Shi J, Deane CM.

Bioinformatics. 2018 Mar 15;34(6):949-956. doi: 10.1093/bioinformatics/btx718.


CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.

Luecken MD, Page MJT, Crosby AJ, Mason S, Reinert G, Deane CM.

Bioinformatics. 2018 Mar 15;34(6):994-1000. doi: 10.1093/bioinformatics/btx706.


STCRDab: the structural T-cell receptor database.

Leem J, de Oliveira SHP, Krawczyk K, Deane CM.

Nucleic Acids Res. 2018 Jan 4;46(D1):D406-D412. doi: 10.1093/nar/gkx971.


In silico structural modeling of multiple epigenetic marks on DNA.

Krawczyk K, Demharter S, Knapp B, Deane CM, Minary P.

Bioinformatics. 2018 Jan 1;34(1):41-48. doi: 10.1093/bioinformatics/btx516.


Variable Regions of Antibodies and T-Cell Receptors May Not Be Sufficient in Molecular Simulations Investigating Binding.

Knapp B, Dunbar J, Alcala M, Deane CM.

J Chem Theory Comput. 2017 Jul 11;13(7):3097-3105. doi: 10.1021/acs.jctc.7b00080. Epub 2017 Jun 28.


Ten simple rules for surviving an interdisciplinary PhD.

Demharter S, Pearce N, Beattie K, Frost I, Leem J, Martin A, Oppenheimer R, Regep C, Rukat T, Skates A, Trendel N, Gavaghan DJ, Deane CM, Knapp B.

PLoS Comput Biol. 2017 May 25;13(5):e1005512. doi: 10.1371/journal.pcbi.1005512. eCollection 2017 May. No abstract available.


Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania.

Parks T, Mirabel MM, Kado J, Auckland K, Nowak J, Rautanen A, Mentzer AJ, Marijon E, Jouven X, Perman ML, Cua T, Kauwe JK, Allen JB, Taylor H, Robson KJ, Deane CM, Steer AC, Hill AVS; Pacific Islands Rheumatic Heart Disease Genetics Network.

Nat Commun. 2017 May 11;8:14946. doi: 10.1038/ncomms14946.


Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

Marks C, Nowak J, Klostermann S, Georges G, Dunbar J, Shi J, Kelm S, Deane CM.

Bioinformatics. 2017 May 1;33(9):1346-1353. doi: 10.1093/bioinformatics/btw823.


A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F.

Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123.


Cross-linking mass spectrometry identifies new interfaces of Augmin required to localise the γ-tubulin ring complex to the mitotic spindle.

Chen JWC, Chen ZA, Rogala KB, Metz J, Deane CM, Rappsilber J, Wakefield JG.

Biol Open. 2017 May 15;6(5):654-663. doi: 10.1242/bio.022905.


Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites.

Pearce NM, Bradley AR, Krojer T, Marsden BD, Deane CM, von Delft F.

Struct Dyn. 2017 Feb 28;4(3):032104. doi: 10.1063/1.4974176. eCollection 2017 May.


The H3 loop of antibodies shows unique structural characteristics.

Regep C, Georges G, Shi J, Popovic B, Deane CM.

Proteins. 2017 Jul;85(7):1311-1318. doi: 10.1002/prot.25291. Epub 2017 Apr 6.


WONKA and OOMMPPAA: analysis of protein-ligand interaction data to direct structure-based drug design.

Deane CM, Wall ID, Green DV, Marsden BD, Bradley AR.

Acta Crystallogr D Struct Biol. 2017 Mar 1;73(Pt 3):279-285. doi: 10.1107/S2059798316009529. Epub 2017 Feb 24.


Antibody H3 Structure Prediction.

Marks C, Deane CM.

Comput Struct Biotechnol J. 2017 Feb 1;15:222-231. doi: 10.1016/j.csbj.2017.01.010. eCollection 2017. Review.


Comparing co-evolution methods and their application to template-free protein structure prediction.

de Oliveira SH, Shi J, Deane CM.

Bioinformatics. 2017 Feb 1;33(3):373-381. doi: 10.1093/bioinformatics/btw618.


Computational Tools for Aiding Rational Antibody Design.

Krawczyk K, Dunbar J, Deane CM.

Methods Mol Biol. 2017;1529:399-416.


The contribution of major histocompatibility complex contacts to the affinity and kinetics of T cell receptor binding.

Zhang H, Lim HS, Knapp B, Deane CM, Aleksic M, Dushek O, van der Merwe PA.

Sci Rep. 2016 Oct 13;6:35326. doi: 10.1038/srep35326.


Modeling Functional Motions of Biological Systems by Customized Natural Moves.

Demharter S, Knapp B, Deane CM, Minary P.

Biophys J. 2016 Aug 23;111(4):710-721. doi: 10.1016/j.bpj.2016.06.028.


Tertiary Element Interaction in HIV-1 TAR.

Krawczyk K, Sim AY, Knapp B, Deane CM, Minary P.

J Chem Inf Model. 2016 Sep 26;56(9):1746-54. doi: 10.1021/acs.jcim.6b00152. Epub 2016 Aug 17.


ABodyBuilder: Automated antibody structure prediction with data-driven accuracy estimation.

Leem J, Dunbar J, Georges G, Shi J, Deane CM.

MAbs. 2016 Oct;8(7):1259-1268. Epub 2016 Jul 8. Erratum in: MAbs. 2018 Apr;10 (3):511-512.


Comparison of large networks with sub-sampling strategies.

Ali W, Wegner AE, Gaunt RE, Deane CM, Reinert G.

Sci Rep. 2016 Jul 6;6:28955. doi: 10.1038/srep28955.


Examining the Conservation of Kinks in Alpha Helices.

Law EC, Wilman HR, Kelm S, Shi J, Deane CM.

PLoS One. 2016 Jun 17;11(6):e0157553. doi: 10.1371/journal.pone.0157553. eCollection 2016.


SAbPred: a structure-based antibody prediction server.

Dunbar J, Krawczyk K, Leem J, Marks C, Nowak J, Regep C, Georges G, Kelm S, Popovic B, Deane CM.

Nucleic Acids Res. 2016 Jul 8;44(W1):W474-8. doi: 10.1093/nar/gkw361. Epub 2016 Apr 29.


Length-independent structural similarities enrich the antibody CDR canonical class model.

Nowak J, Baker T, Georges G, Kelm S, Klostermann S, Shi J, Sridharan S, Deane CM.

MAbs. 2016 May-Jun;8(4):751-60. doi: 10.1080/19420862.2016.1158370.


T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex.

Knapp B, Deane CM.

J Chem Inf Model. 2016 Jan 25;56(1):46-53. doi: 10.1021/acs.jcim.5b00511. Epub 2015 Dec 29.


Rapid, Precise, and Reproducible Prediction of Peptide-MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment.

Wan S, Knapp B, Wright DW, Deane CM, Coveney PV.

J Chem Theory Comput. 2015 Jul 14;11(7):3346-56. doi: 10.1021/acs.jctc.5b00179. Epub 2015 Jun 24.


ANARCI: antigen receptor numbering and receptor classification.

Dunbar J, Deane CM.

Bioinformatics. 2016 Jan 15;32(2):298-300. doi: 10.1093/bioinformatics/btv552. Epub 2015 Sep 30.


Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.

Knapp B, Demharter S, Deane CM, Minary P.

Bioinformatics. 2016 Jan 15;32(2):181-6. doi: 10.1093/bioinformatics/btv502. Epub 2015 Sep 22.


WONKA: objective novel complex analysis for ensembles of protein-ligand structures.

Bradley AR, Wall ID, von Delft F, Green DV, Deane CM, Marsden BD.

J Comput Aided Mol Des. 2015 Oct;29(10):963-73. doi: 10.1007/s10822-015-9866-z. Epub 2015 Sep 19.


Structural Bridges through Fold Space.

Edwards H, Deane CM.

PLoS Comput Biol. 2015 Sep 15;11(9):e1004466. doi: 10.1371/journal.pcbi.1004466. eCollection 2015 Sep.


Type II Inhibitors Targeting CDK2.

Alexander LT, Möbitz H, Drueckes P, Savitsky P, Fedorov O, Elkins JM, Deane CM, Cowan-Jacob SW, Knapp S.

ACS Chem Biol. 2015 Sep 18;10(9):2116-25. doi: 10.1021/acschembio.5b00398. Epub 2015 Jul 20.


Misato Controls Mitotic Microtubule Generation by Stabilizing the TCP-1 Tubulin Chaperone Complex [corrected].

Palumbo V, Pellacani C, Heesom KJ, Rogala KB, Deane CM, Mottier-Pavie V, Gatti M, Bonaccorsi S, Wakefield JG.

Curr Biol. 2015 Jun 29;25(13):1777-83. doi: 10.1016/j.cub.2015.05.033. Epub 2015 Jun 18. Erratum in: Curr Biol. 2015 Aug 3;25(15):2063.


The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation.

Rogala KB, Dynes NJ, Hatzopoulos GN, Yan J, Pong SK, Robinson CV, Deane CM, Gönczy P, Vakonakis I.

Elife. 2015 May 29;4:e07410. doi: 10.7554/eLife.07410.

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