2024:
Pred-O3, a web server to predict molecules, olfactory receptors and odor relationships.

Ollitrault G, Achebouche R, Dreux A, Murail S, Audouze K, Tromelin A, Taboureau O. Nucleic Acids Res. 2024 Jul 5;52(W1):W507-W512. doi: 10.1093/nar/gkae305. PMID: 38661190
A Machine Learning Approach to Identify Key Residues Involved in Protein-Protein Interactions Exemplified with SARS-CoV-2 Variants.

Quitté L, Leclercq M, Prunier J, Scott-Boyer MP, Moroy G, Droit A. Int J Mol Sci. 2024 Jun 13;25(12):6535. doi: 10.3390/ijms25126535. PMID: 38928241
Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein.

Ghoula M, Deyawe Kongmeneck A, Eid R, Camproux AC, Moroy G. J Phys Chem B. 2023 Oct 12;127(40):8586-8602. doi: 10.1021/acs.jpcb.3c01467. Epub 2023 Sep 29. PMID: 37775095

Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization.

Karami Y, Murail S, Giribaldi J, Lefranc B, Defontaine F, Lesouhaitier O, Leprince J, de Vries S, Tufféry P. J Chem Inf Model. 2023 Oct 23;63(20):6436-6450. doi: 10.1021/acs.jcim.3c00865. Epub 2023 Oct 12. PMID: 37827517

Evolutionarily conserved protein motifs drive interactions between the plant nucleoskeleton and nuclear pores.

Mermet S, Voisin M, Mordier J, Dubos T, Tutois S, Tuffery P, Baroux C, Tamura K, Probst AV, Vanrobays E, Tatout C. Plant Cell. 2023 Nov 30;35(12):4284-4303. doi: 10.1093/plcell/koad236. PMID: 37738557
Identifying promising druggable binding sites and their flexibility to target the receptor-binding domain of SARS-CoV-2 spike protein.

Ghoula M, Naceri S, Sitruk S, Flatters D, Moroy G, Camproux AC. Comput Struct Biotechnol J. 2023;21:2339-2351. doi: 10.1016/j.csbj.2023.03.029. Epub 2023 Mar 18. PMID: 36998674

DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion.

Barbault F, Brémond E, Rey J, Tufféry P, Maurel F. J Chem Inf Model. 2023 Aug 28;63(16):5220-5231. doi: 10.1021/acs.jcim.3c00569. Epub 2023 Aug 14. PMID: 37579187

PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution.

Rey J, Murail S, de Vries S, Derreumaux P, Tuffery P. Nucleic Acids Res. 2023 Jul 5;51(W1):W432-W437. doi: 10.1093/nar/gkad376. PMID: 37166962

In Silico and In Vivo Studies of a Tumor-Penetrating and Interfering Peptide with Antitumoral Effect on Xenograft Models of Breast Cancer.

Marin GH, Murail S, Andrini L, Garcia M, Loisel S, Tuffery P, Rebollo A. Pharmaceutics. 2023 Apr 7;15(4):1180. doi: 10.3390/pharmaceutics15041180. PMID: 37111665

A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution.

Tufféry P, Derreumaux P. Front Bioinform. 2023 Jan 16;3:1113928. doi: 10.3389/fbinf.2023.1113928. eCollection 2023. PMID: 36727106

Binding and Kinetic Analysis of Human Protein Phosphatase PP2A Interactions with Caspase 9 Protein and the Interfering Peptide C9h.

Dorgham K, Murail S, Tuffery P, Savier E, Bravo J, Rebollo A. Pharmaceutics. 2022 Sep 27;14(10):2055. doi: 10.3390/pharmaceutics14102055. PMID: 36297489

Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.

Nguyen PH, Tufféry P, Derreumaux P. Methods Mol Biol. 2022;2405:95-113. doi: 10.1007/978-1-0716-1855-4_5. PMID: 35298810

A Generalized Attraction-Repulsion Potential and Revisited Fragment Library Improves PEP-FOLD Peptide Structure Prediction.

Binette V, Mousseau N, Tuffery P. J Chem Theory Comput. 2022 Apr 12;18(4):2720-2736. doi: 10.1021/acs.jctc.1c01293. Epub 2022 Mar 17. PMID: 35298162

PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions?

Rebollo A, Fliedel L, Tuffery P. Biomolecules. 2022 Jan 21;12(2):178. doi: 10.3390/biom12020178. PMID: 35204680
Isolation of Primary Hepatocytes for Testing Tumor Penetrating Peptides.

Savier E, Tuffery P, Bruzzoni-Giovanelli H, Rebollo A. Methods Mol Biol. 2022;2383:413-427. doi: 10.1007/978-1-0716-1752-6_26. PMID: 34766304