Charlotte M. Deane

According to our database1, Charlotte M. Deane authored at least 62 papers between 1998 and 2019.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.



In proceedings 
PhD thesis 





Assessment of model fit via network comparison methods based on subgraph counts.
J. Complex Networks, 2019

SCALOP: sequence-based antibody canonical loop structure annotation.
Bioinformatics, 2019

STCRDab: the structural T-cell receptor database.
Nucleic Acids Research, 2018

Identifying networks with common organizational principles.
J. Complex Networks, 2018

Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.
Bioinformatics, 2018

Combining co-evolution and secondary structure prediction to improve fragment library generation.
Bioinformatics, 2018

Predicting loop conformational ensembles.
Bioinformatics, 2018

CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.
Bioinformatics, 2018

In silico structural modeling of multiple epigenetic marks on DNA.
Bioinformatics, 2018

pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions.
Bioinformatics, 2018

Ten simple rules for surviving an interdisciplinary PhD.
PLoS Computational Biology, 2017

Comparing co-evolution methods and their application to template-free protein structure prediction.
Bioinformatics, 2017

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.
Bioinformatics, 2017

SAbPred: a structure-based antibody prediction server.
Nucleic Acids Research, 2016

Tertiary Element Interaction in HIV-1 TAR.
Journal of Chemical Information and Modeling, 2016

T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex.
Journal of Chemical Information and Modeling, 2016

Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.
Bioinformatics, 2016

ANARCI: antigen receptor numbering and receptor classification.
Bioinformatics, 2016

Progress and challenges in predicting protein interfaces.
Briefings in Bioinformatics, 2016

Ten Simple Rules for a Successful Cross-Disciplinary Collaboration.
PLoS Computational Biology, 2015

Structural Bridges through Fold Space.
PLoS Computational Biology, 2015

WONKA: objective novel complex analysis for ensembles of protein-ligand structures.
Journal of Computer-Aided Molecular Design, 2015

Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations.
Briefings in Bioinformatics, 2015

Ten Simple Rules for Effective Computational Research.
PLoS Computational Biology, 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 Computational Biology, 2014

Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design.
PLoS Computational Biology, 2014

SAbDab: the structural antibody database.
Nucleic Acids Research, 2014

Crowdsourcing Yields a New Standard for Kinks in Protein Helices.
Journal of Chemical Information and Modeling, 2014

OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data.
Journal of Chemical Information and Modeling, 2014

Gro2mat: A package to efficiently read gromacs output in MATLAB.
Journal of Computational Chemistry, 2014

Improving B-cell epitope prediction and its application to global antibody-antigen docking.
Bioinformatics, 2014

Alignment-free protein interaction network comparison.
Bioinformatics, 2014

Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies.
PLoS Computational Biology, 2013

Memoir: template-based structure prediction for membrane proteins.
Nucleic Acids Research, 2013

MP-T: improving membrane protein alignment for structure prediction.
Bioinformatics, 2013

What Evidence Is There for the Homology of Protein-Protein Interactions?
PLoS Computational Biology, 2012

Freely Available Conformer Generation Methods: How Good Are They?
Journal of Chemical Information and Modeling, 2012

The Importance of Age and High Degree, in Protein-Protein Interaction Networks.
Journal of Computational Biology, 2012

Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains.
Adv. Bioinformatics, 2012

Environment specific substitution tables improve membrane protein alignment.
Bioinformatics [ISMB/ECCB], 2011

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks.
PLoS Computational Biology, 2010

The function of communities in protein interaction networks at multiple scales.
BMC Systems Biology, 2010

Deciphering chemotaxis pathways using cross species comparisons.
BMC Systems Biology, 2010

Directionality in protein fold prediction.
BMC Bioinformatics, 2010

How threshold behaviour affects the use of subgraphs for network comparison.
Bioinformatics, 2010

Exploring the potential of template-based modelling.
Bioinformatics, 2010

MEDELLER: homology-based coordinate generation for membrane proteins.
Bioinformatics, 2010

iMembrane: homology-based membrane-insertion of proteins.
Bioinformatics, 2009

Functionally guided alignment of protein interaction networks for module detection.
Bioinformatics, 2009

Predicting and Validating Protein Interactions Using Network Structure.
PLoS Computational Biology, 2008

An assessment of the uses of homologous interactions.
Bioinformatics, 2008

Using Phylogeny to Improve Genome-Wide Distant Homology Recognition.
PLoS Computational Biology, 2007

Using the protein interaction network to predict protein folds without homology.
BMC Systems Biology, 2007

Linking evolution of protein structures through fragments.
BMC Systems Biology, 2007

A statistical approach using network structure in the prediction of protein characteristics.
Bioinformatics, 2007

Cotranslational protein folding - fact or fiction?
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

Protein protein interactions, evolutionary rate, abundance and age.
BMC Bioinformatics, 2006

Modelling sequential protein folding under kinetic control.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

How old is your fold?
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

SCORE: predicting the core of protein models.
Bioinformatics, 2001

Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure.
Bioinformatics, 2000

JOY: protein sequence-structure representation and analysis.
Bioinformatics, 1998