Publications of RPBS team


De Vries SJ, Rey J, Schindler CEM, Zacharias M, Tuffery P.
The pepATTRACT web server for blind, large-scale peptide-protein docking.
Nucleic Acids Res. 2017 Apr 29.


Lamiable A, Thévenet P, Rey J, Vavrusa M, Derreumaux P, Tufféry P.
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex.
Nucleic Acids Res. 2016 Jul 8;44(W1):W449-54.
Yu J, Vavrusa M, Andreani J, Rey J, Tufféry P, Guerois R.
InterEvDock: A docking server to predict the structure of protein-protein interactions using evolutionary information.
Nucleic Acids Res. 2016 Jul 8;44(W1):W542-9.


Yu J, Picord G, Tufféry P, Guerois R.
HHalign-KBest: exploring sub-optimal alignments for remote homology comparative modeling
Bioinformatics. 2015 Dec 1;31(23):3850-2.
Labbé C, Rey J, Lagorce D, Vavruša M, Becot J, Sperandio O, Villoutreix B, Tufféry P, Miteva M.
MTiOpenScreen: a web server for structure-based virtual screening.
Nucleic Acids Res. 2015 Jul 1;43(W1):W448-54.
Guyon F, Martz F, Vavruša M, Bécot J, Rey J, Tufféry P.
BCSearch: fast structural fragment mining over large collections of protein structures.
Nucleic Acids Res. 2015 Jul 1;43(W1):W378-82.


Rey J, Deschavanne P, Tufféry P.
BactPepDB: a database of predicted peptides from an exhaustive survey of complete prokaryote genomes.
Database (Oxford). 2014 Nov 6;2014. Print 2014.
Saladin A, Rey J, Thévenet P, Zacharias M, Moroy G, Tufféry P.
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W221-6.
Shen Y, Maupetit J, Derreumaux P, Tufféry P.
Improved PEP-FOLD approach for peptide and miniprotein structure prediction
J. Chem. Theor. Comput. 2014; 10:4745-4758
Guyon F, Tufféry P.
Fast protein fragment similarity scoring using a Binet-Cauchy kernel.
Bioinformatics. 2014 Mar 15;30(6):784-91.


Shen Y, Picord G, Guyon F, Tuffery P.
Detecting protein candidate fragments using a structural alphabet profile comparison approach.
PLoS One. 2013 Nov 26;8(11).


Thévenet P, Shen Y, Maupetit J, Guyon F, Derreumaux P, Tufféry P.
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W288-93.
Feriotto G, Calza R, Bergamini CM, Griffin M, Wang Z, Beninati S, Ferretti V, Marzola E, Guerrini R, Pagnoni A, Cavazzini A, Casciano F, Mischiati C.
Involvement of cell surface TG2 in the aggregation of K562 cells triggered by gluten.
Amino Acids. 2017 Mar;49(3):551-565.
de la Rosa G, Pastor N, Alagón A, Corzo G.
Synthetic peptide antigens derived from long-chain alpha-neurotoxins: Immunogenicity effect against elapid venoms.
Peptides. 2017 Feb;88:80-86.
Tang M, Li T, Gandhi NS, Burrage K, Gu Y.
Heterogeneous nanomechanical properties of type I collagen in longitudinal direction.
Biomech Model Mechanobiol. 2017 Jan 7.
Dale JB, Smeesters PR, Courtney HS, Penfound TA, Hohn CM, Smith JC, Baudry JY.
Structure-based design of broadly protective group a streptococcal M protein-based vaccines.
Vaccine. 2017 Jan 3;35(1):19-26.
Hanazono Y, Takeda K, Miki K.
Structural studies of the N-terminal fragments of the WW domain: Insights into co-translational folding of a beta-sheet protein.
Sci Rep. 2016 Oct 4;6:34654.
Barthe P, Veyron-Churlet R, de Visch A, Gilleron M, Saliou JM, Tomavo S, Nigou J, Brodin P, Cohen-Gonsaud M.
Mycobacterium tuberculosis LppM Displays an Original Structure and Domain Composition Linked to a Dual Localization.
Structure. 2016 Oct 4;24(10):1788-1794.
Babbitt SE, Hsu J, Kranz RG.
Molecular Basis Behind Inability of Mitochondrial Holocytochrome c Synthase to Mature Bacterial Cytochromes: DEFINING A CRITICAL ROLE FOR CYTOCHROME c α HELIX-1.
J Biol Chem. 2016 Aug 19;291(34):17523-34.
Bornholdt ZA, Turner HL, Murin CD, Li W, Sok D, Souders CA, Piper AE, Goff A, Shamblin JD, Wollen SE, Sprague TR, Fusco ML, Pommert KB, Cavacini LA, Smith HL, Klempner M, Reimann KA, Krauland E, Gerngross TU, Wittrup KD, Saphire EO, Burton DR, Glass PJ, Ward AB, Walker LM.
Isolation of potent neutralizing antibodies from a survivor of the 2014 Ebola virus outbreak.
Science. 2016 Mar 4;351(6277):1078-83.
Han HM, Gopal R, Park Y.
Design and membrane-disruption mechanism of charge-enriched AMPs exhibiting cell selectivity, high-salt resistance, and anti-biofilm properties.
Amino Acids. 2016 Feb;48(2):505-22.