Structural symmetry and protein function, Annual Review of Biophysics and Biomolecular Structure, vol.29, 2000. ,
The biological effects of simple tandem repeats: lessons from the repeat expansion diseases, Genome Research, vol.18, pp.1011-1019, 2008. ,
Tandem repeats mediating genetic plasticity in health and disease, Nature Reviews Genetics, vol.19, pp.286-298, 2018. ,
Rational design of ?-helical tandem repeat proteins with closed architectures, Nature, vol.528, issue.7583, p.585, 2015. ,
DOI : 10.1038/nature16191
URL : http://europepmc.org/articles/pmc4727831?pdf=render
Evolutioninspired computational design of symmetric proteins, Computational Protein Design, pp.309-322, 2017. ,
Accurate design of megadalton-scale two-component icosahedral protein complexes, Science, vol.353, issue.6297, pp.389-394, 2016. ,
Analytical symmetry detection in protein assemblies. I. Cyclic symmetries, Journal of Structural Biology, vol.203, issue.2, pp.142-148, 2018. ,
Analytical symmetry detection in protein assemblies. II. Dihedral and cubic symmetries, Journal of Structural Biology, vol.203, issue.3, pp.185-194, 2018. ,
Tandem repeats in proteins: from sequence to structure, Journal of Structural Biology, vol.179, issue.3, pp.279-288, 2012. ,
Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance, Briefings in Bioinformatics, vol.14, issue.1, pp.67-81, 2012. ,
Tandem repeats in proteins: prediction algorithms and biological role, Frontiers in Bioengineering and Biotechnology, vol.3, p.143, 2015. ,
DOI : 10.3389/fbioe.2015.00143
URL : https://www.frontiersin.org/articles/10.3389/fbioe.2015.00143/pdf
Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Research, vol.27, issue.2, p.573, 1999. ,
DOI : 10.1093/nar/27.2.573
URL : https://academic.oup.com/nar/article-pdf/27/2/573/6268426/27-2-573.pdf
TROLL-tandem repeat occurrence locator, Bioinformatics, vol.18, issue.4, pp.634-636, 2002. ,
mreps: Efficient and flexible detection of tandem repeats in dna, Nucleic Acids Research, vol.31, issue.13, pp.3672-3678, 2003. ,
DOI : 10.1093/nar/gkg617
URL : https://hal.archives-ouvertes.fr/inria-00099597
Xstream: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences, BMC Bioinformatics, vol.8, issue.1, p.382, 2007. ,
Toward the detection and validation of repeats in protein structure, Proteins: Structure, Function, and Bioinformatics, vol.57, issue.2, pp.365-380, 2004. ,
Alternative alignments from comparison of protein structures, Proteins: Structure, Function, and Bioinformatics, vol.56, issue.3, pp.519-527, 2004. ,
Swelfe: a detector of internal repeats in sequences and structures, Bioinformatics, vol.24, issue.13, pp.1536-1537, 2008. ,
URL : https://hal.archives-ouvertes.fr/pasteur-00336123
Systematic detection of internal symmetry in proteins using ce-symm, Journal of Molecular Biology, vol.426, issue.11, pp.2255-2268, 2014. ,
Detecting internally symmetric protein structures, BMC Bioinformatics, vol.11, issue.1, p.303, 2010. ,
DOI : 10.1186/1471-2105-11-303
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-303
TAPO: A combined method for the identification of tandem repeats in protein structures, FEBS Letters, vol.589, issue.19, pp.2611-2619, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01883461
RepeatsDB: a database of tandem repeat protein structures, Nucleic Acids Research, vol.42, issue.D1, pp.352-357, 2013. ,
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures, Nucleic Acids Research, vol.45, issue.D1, pp.308-312, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01875237
Identification of repetitive units in protein structures with ReUPred, Amino Acids, vol.48, issue.6, pp.1391-1400, 2016. ,
, Pattern Recognition and Machine Learning, 2006.
Full and partial symmetries of non-rigid shapes, International Journal of Computer Vision, vol.89, issue.1, pp.18-39, 2010. ,
Global intrinsic symmetries of shapes, Computer Graphics Forum, vol.27, issue.5, pp.1341-1348, 2008. ,
Symmetry in 3D geometry: Extraction and applications, Computer Graphics Forum, vol.32, issue.6, pp.1-23, 2013. ,
Imagenet classification with deep convolutional neural networks, Advances in Neural Information Processing Systems, pp.1097-1105, 2012. ,
DeepQA: improving the estimation of single protein model quality with deep belief networks, BMC Bioinformatics, vol.17, issue.1, p.495, 2016. ,
Accurate de novo prediction of protein contact map by ultra-deep learning model, PLoS Computational Biology, vol.13, issue.1, p.1005324, 2017. ,
DNCON2: Improved protein contact prediction using two-level deep convolutional neural networks, Bioinformatics, vol.34, issue.9, pp.1466-1472, 2018. ,
The human splicing code reveals new insights into the genetic determinants of disease, Science, vol.347, issue.6218, p.1254806, 2015. ,
Predicting effects of noncoding variants with deep learning-based sequence model, Nature Methods, vol.12, issue.10, p.931, 2015. ,
Quantum-chemical insights from deep tensor neural networks, Nature Communications, vol.8, p.13890, 2017. ,
Machine learning of accurate energy-conserving molecular force fields, Science Advances, vol.3, issue.5, p.1603015, 2017. ,
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost, Chemical Science, vol.8, issue.4, pp.3192-3203, 2017. ,
Deep convolutional networks for quality assessment of protein folds, Bioinformatics, p.494, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01702857
Protein model quality assessment using 3D oriented convolutional neural networks. bioRxiv, p.432146, 2018. ,
3D deep convolutional neural networks for amino acid environment similarity analysis, BMC Bioinformatics, vol.18, issue.1, p.302, 2017. ,
KDEEP: Protein-ligand absolute binding affinity prediction via 3D-convolutional neural networks, Journal of Chemical Information and Modeling, vol.58, issue.2, pp.287-296, 2018. ,
Visualizing convolutional neural network protein-ligand scoring, Journal of Molecular Graphics and Modelling, vol.84, pp.96-108, 2018. ,
DeepSite: protein-binding site predictor using 3D-convolutional neural networks, Bioinformatics, vol.33, issue.19, pp.3036-3042, 2017. ,
EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation, 2017. ,
Delving deep into rectifiers: Surpassing human-level performance on imagenet classification, Proceedings of the IEEE International Conference on Computer Vision, pp.1026-1034, 2015. ,
Immersing projective spaces, Annals of Mathematics, pp.473-482, 1967. ,
Multilayer feedforward networks are universal approximators, Neural networks, vol.2, issue.5, pp.359-366, 1989. ,
The Protein Data Bank, Nucleic Acids Research, vol.28, pp.235-242, 2000. ,
SchNet: A continuous-filter convolutional neural network for modeling quantum interactions, Advances in Neural Information Processing Systems, pp.992-1002, 2017. ,
Tensor field networks: Rotation-and translation-equivariant neural networks for 3D point clouds, 2018. ,
Harmonic networks: Deep translation and rotation equivariance, IEEE Conference on Computer Vision and Pattern Recognition (CVPR), vol.2, 2017. ,
Structure validation by C? geometry: ?, ? and c? deviation, Proteins: Structure, Function, and Bioinformatics, vol.50, issue.3, pp.437-450, 2003. ,
An image synthesizer, ACM Siggraph Computer Graphics, vol.19, issue.3, pp.287-296, 1985. ,
Improving neural networks by preventing co-adaptation of feature detectors, 2012. ,
Adam: A method for stochastic optimization, 2014. ,
Tensorflow: a system for large-scale machine learning, Proceedings of the 12th USENIX conference on Operating Systems Design and Implementation, pp.265-283, 2016. ,