RNA and disease, Cell, vol.136, pp.777-793, 2009. ,
RNA recognition motifs: boring? Not quite, Curr Opin Struct Biol, vol.18, pp.290-298, 2008. ,
Crystallization of RNA and RNA-protein complexes, Methods, vol.34, pp.408-414, 2004. ,
RNA structure determination by NMR, Methods Mol Biol, vol.452, pp.29-61, 2008. ,
NMR studies of protein-RNA interactions, Methods Mol Biol, vol.831, pp.197-218, 2012. ,
Protein families and RNA recognition, FEBS J, vol.272, pp.2088-2097, 2005. ,
Protein-RNA interactions: structural analysis and functional classes, Proteins, vol.66, pp.903-911, 2007. ,
Small-angle X-ray scattering from RNA, proteins, and protein complexes, Annu Rev Biophys Biomol Struct, vol.36, pp.307-327, 2007. ,
Protein-RNA interactions: new genomic technologies and perspectives, Nat Rev Genet, vol.13, pp.77-83, 2011. ,
Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing, Semin Cell Dev Biol, vol.23, pp.206-212, 2012. ,
Towards atomic resolution structural determination by singleparticle cryo-electron microscopy, Curr Opin Struct Biol, vol.18, pp.218-228, 2008. ,
Engineering RNA-binding proteins for biology, FEBS J, vol.280, pp.3734-3754, 2013. ,
Computational methods for prediction of protein-RNA interactions, J Struct Biol, vol.179, pp.261-268, 2012. ,
Assessment of blind predictions of protein-protein interactions: current status of docking methods, Proteins, vol.52, pp.51-67, 2003. ,
Predicting 3D structures of protein-protein complexes, Curr Pharm Biotechnol, vol.9, pp.57-66, 2008. ,
Protein-protein docking dealing with the unknown, J Comput Chem, vol.31, pp.317-342, 2010. ,
Protein-protein docking tested in blind predictions: the CAPRI experiment, Mol Biosyst, vol.6, pp.2351-2362, 2010. ,
Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions, Proteins, vol.78, pp.3242-3249, 2010. ,
Community-wide assessment of protein-interface modeling suggests improvements to design methodology, J Mol Biol, vol.414, pp.289-302, 2011. ,
URL : https://hal.archives-ouvertes.fr/inria-00637848
Blind prediction of interfacial water positions in CAPRI, Proteins, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00880345
Docking, scoring, and affinity prediction in CAPRI, Proteins, vol.81, pp.2082-2095, 2013. ,
Automated de novo prediction of native-like RNA tertiary structures, Proc Natl Acad Sci U S A, vol.104, pp.14664-14669, 2007. ,
Atomic accuracy in predicting and designing noncanonical RNA structure, Nat Methods, vol.7, pp.291-294, 2010. ,
Computational approaches to 3D modeling of RNA, J Phys Condens Matter, vol.22, p.283101, 2010. ,
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data, Nature, vol.452, pp.51-55, 2008. ,
RNA and protein 3D structure modeling: similarities and differences, J Mol Model, vol.17, pp.2325-2336, 2011. ,
Multiscale modeling of macromolecular biosystems, Brief Bioinform, vol.13, pp.395-405, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00684530
A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys, Nucleic Acids Res, vol.32, pp.5147-5162, 2004. ,
A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method, Nucleic Acids Res, 2014. ,
Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials, Pac Symp Biocomput, pp.293-301, 2010. ,
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking, BMC Bioinformatics, vol.12, p.348, 2011. ,
A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins, FEBS J, vol.274, pp.6378-6391, 2007. ,
A new residue-nucleotide propensity potential with structural information considered for discriminating protein-RNA docking decoys, Proteins, vol.80, pp.14-24, 2012. ,
A coarse-grained force field for Protein-RNA docking, Nucleic Acids Res, vol.39, pp.9118-9129, 2011. ,
PRIDB: a Protein-RNA interface database, Nucleic Acids Res, vol.39, pp.277-282, 2011. ,
A protein-RNA docking benchmark (I): nonredundant cases, Proteins, vol.80, pp.1866-1871, 2012. ,
A nonredundant structure dataset for benchmarking protein-RNA computational docking, J Comput Chem, vol.34, pp.311-318, 2013. ,
A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data, Proteins, vol.80, pp.1872-1882, 2012. ,
Using Kendall-t Meta-Bagging to Improve Protein-Protein Docking Predictions, Pattern Recognition in Bioinformatics, pp.284-295, 2011. ,
A new protein-protein docking scoring function based on interface residue properties, Bioinformatics, vol.23, pp.555-562, 2007. ,
URL : https://hal.archives-ouvertes.fr/inria-00431697
A docking analysis of the statistical physics of protein-protein recognition, Phys Biol, vol.2, pp.17-23, 2005. ,
URL : https://hal.archives-ouvertes.fr/inria-00431699
Protein docking using surface matching and supervised machine learning, Proteins, vol.68, pp.488-502, 2007. ,
A collaborative filtering approach for protein-protein docking scoring functions, PLoS One, vol.6, p.18541, 2011. ,
URL : https://hal.archives-ouvertes.fr/inria-00625000
Improving ranking of models for protein complexes with side chain modeling and atomic potentials, Proteins, vol.81, pp.592-606, 2013. ,
Data-driven models for protein interaction and design, Proteins, vol.81, pp.2221-2228, 2013. ,
High-resolution protein-protein docking, Curr Opin Struct Biol, vol.16, pp.183-193, 2006. ,
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations, J Mol Biol, vol.331, pp.281-299, 2003. ,
Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds, Proteins, vol.81, pp.2201-2209, 2013. ,
Rosetta in CAPRI rounds 13-19, Proteins, vol.78, pp.3212-3218, 2010. ,
Docking and scoring protein complexes: CAPRI 3rd Edition, Proteins, vol.69, pp.704-718, 2007. ,
An improved protein decoy set for testing energy functions for protein structure prediction, Proteins, vol.53, pp.76-87, 2003. ,
Fully differentiable coarsegrained and all-atom knowledge-based potentials for RNA structure evaluation, RNA, vol.17, pp.1066-1075, 2011. ,
URL : https://hal.archives-ouvertes.fr/inria-00624999
Evaluating mixture models for building RNA knowledge-based potentials, J Bioinform Comput Biol, vol.10, p.1241010, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00757761
Apprentissage de fonctions de tri pour la prédiction d'interactions protéine-ARN, pp.479-484, 2014. ,
Characterizing RNA ensembles from NMR data with kinematic models, Nucleic Acids Res, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01058971
MetalionRNA: computational predictor of metal-binding sites in RNA structures, Bioinformatics, vol.28, pp.198-205, 2012. ,