Exploitation of the information contained in the protein sequences
Protein folding rules
Selected publications

The HCA method - methodology

Deciphering protein sequence information though hydrohobic cluster analysis. Current status and perspectives. Callebaut I, Labesse G, Durand P, Poupon A, Canard L, Chomilier J, Henrissat B., Mornon JP. Cell. Mol. Life Sci. (1997) 53, 621-645

Detection of secondary structure elements in proteins by hydrophobic cluster analysis. Woodcock S, Mornon JP, Henrissat B. Protein Eng (1992) 5 (7): 629-635

Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences. Lemesle-Varloot L, Henrissat B, Gaboriaud C, Bissery V, Morgat A, Mornon JP. Biochimie (1990) 72 (8): 555-574

Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. Gaboriaud C, Bissery V, Benchetrit T, Mornon JP. FEBS Lett (1987) 224 (1): 149-155

Sequence analysis and the HCA method - applications

of particular interest relative to the HCA method

Sequence analysis identifies a ras-associating (RA)-like domain in the N-termini of band 4.1/JEF domains and in the Grb7/10/14 adapter family. Wojcik J, Girault JA, Labesse G, Chomilier J, Mornon JP, Callebaut I Biochem Biophys Res Commun (1999) 259(1):113-20

Molecular cloning, expression analysis, and chromosomal localization of human syntaxin 8 (STX8). Thoreau V, Berges T, Callebaut I, Guillier-Gencik Z, Gressin L, Bernheim A, Karst F, Mornon JP, Kitzis A, Chomel JC Biochem Biophys Res Commun (1999) 257(2):577-83

Halaby DM, Poupon A, Mornon JP The immunoglobulin fold family: sequence analysis and 3D structure comparisons. Protein Eng (1999) 12(7):563-71

The BAH (bromo-adjacent homology) domain: a link between DNA methylation, replication and transcriptional regulation Callebaut I, Courvalin JC, Mornon JP Febs Lett (1999) 446 (1):189-93

The N-termini of FAK and JAKs contain divergent band 4.1 domains. Girault JA, Labesse G, Mornon JP, Callebaut I Trends Biochem. Sci. (1999) 24(2):54-7

Janus kinases and focal adhesion kinases play in the 4.1 band: A superfamily of band 4.1 domains important for cell structure and signal transduction.Girault JA, Labesse G, Mornon JP, Callebaut I Mol Med (1998) 4(12):751-69

An homologue of the human 100-kDa protein (p100) is differentially expressed by Histoplasma capsulatum during infection of murine macrophages.Porta A, Colonna-Romano S, Callebaut I, Franco A, Marzullo L, Kobayashi GS, Maresca B Biochem Biophys Res Commun (1999) 254(3):605-13

EVH1/WH1 domains of VASP and WASP proteins belong to a large family including Ran-binding domains of the RanBP1 family.Callebaut I, Cossart P, Dehoux P FEBS Lett (1998) 441(2):181-5

The characterization of murine BCMA gene defines it as a new member of the tumor necrosis factor receptor superfamily.Madry C, Laabi Y, Callebaut I, Roussel J, Hatzoglou A, Le Coniat M, Mornon JP, Berger R, Tsapis A Int Immunol (1998) 10(11):1693-702

Functional and structural characterization of the prp3 binding domain of the yeast prp4 splicing factor.Ayadi L, Callebaut I, Saguez C, Villa T, Mornon JP, Banroques J J Mol Biol (1998) 284(3):673-87

Kx, a quantitatively minor protein from human erythrocytes, is palmitoylated in vivo.Carbonnet F, Hattab C, Callebaut I, Cochet S, Blancher A, Cartron JP, Bertrand O Biochem Biophys Res Commun (1998) 250(3):569-74

The V(D)J recombination activating protein RAG2 consists of a six-bladed propeller and a PHD-fingerlike domain, as revealed by sequence analysis. Callebaut I, Mornon JP. Cell. Mol. Life Sci. (1998)54 : 880-891

Alpha-Crystallin C-terminal domain: on the track of an Ig fold. Mornon JP, Halaby D, Malfois M, Durand P, Callebaut I, Tardieu A. Int J Biol Macromol. (1998) 22 (3-4): 219-227.

Conservative Mutations in the Immunosuppressive Region of the Bovine Leukemia Virus Transmembrane Protein Affect Fusion but Not Infectivity in Vivo. Gatot JS, Callebaut I, Mornon JP, Portetelle D, Burny A, Kerkhofs P, Kettmann R, Willems L J Biol Chem (1998) 273(21):12870-12880

The immunoglobulin superfamily: an insight on its tissular, species, and functional diversity. Halaby DM, Mornon JP J Mol Evol (1998) 46(4):389-400

Sequence and 3D structural relationships between mammalian Ras- and Rho-specific GTPase-activating proteins (GAPs): the cradle fold. Calmels TPG, Callebaut I, Léger I, Durand P, Bril A., Mornon JP, Souchet M. FEBS Lett. (1998) 426(2): 205-211

Hydrophobic cluster analysis reveals a third chromodomain in the Tetrahymena Pdd1p protein of the chromo superfamily. Callebaut I, Courvalin JC, Worman HJ, Mornon JP Biochem Biophys Res Commun (1997) 235(1), 103-107

From BRCA1 to RAP1: a widespread BRCT module closely associated to DNA repair. Callebaut I, Mornon JP FEBS Letters (1997) 400 (1): 25-30.

The EBNA-2 coactivator p100: multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development. Callebaut I , Mornon JP Biochem J (1997) 321 (1): 125-132

Domain-specific interactions of human HP1-type chromodomain proteins and inner nuclear membrane protein LBR. Ye Q, Callebaut I, Pezhman A, Courvalin JC, Worman HJ J Biol Chem (1997) 272 (23): 14983-14989

Active-site motifs of lysosomal acid hydrolases: invariant features of Clan GH-A glycosyl hydrolases deduced from Hydrophobic Cluster Analysis. Durand P, Lehn P, Callebaut I, Fabrega S, Henrissat B, Mornon JP Glycobiology (1997) 7 (2): 277-284

Cloning of a new murine endogenous retrovirus, MuERV-L, with strong similarity to the human HERV-L element and with a gag coding sequence closely related to the Fv1 restriction gene. Benit L, De Parseval N, Casella JF, Callebaut I, Cordonnier A, Heidmann T J Virol (1997) 71 (7): 5652-5657

Homology modeling of rabbit prolactin hormone complexed with its receptor. Halaby D, Thoreau E, Djiane J, Mornon JP Proteins (1997) 27 (3): 459-468

Identification of cytoplasmic motifs required for short prolactin receptor internalization.Vincent V, Goffin V, Rozakis-Adcock M, Mornon JP, Kelly PA J Biol Chem (1997) 272 (11): 7062-7068

A novel plant peptidyl-prolyl-cis-trans-isomerase (PPIase): cDNA cloning, structural analysis, enzymatic activity and expression. Blecher O, Erel N, Callebaut I, Aviezer K, Breiman A Plant Mol Biol (1996) 32 (3): 493-504

Trigger factor,one of the Escherichia coli chaperone proteins, is an original member of the FKBP family. Callebaut I, Mornon JP FEBS Letters (1995) 374:211-215

Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases.Henrissat B, Callebaut I, Fabrega S, Lehn P, Mornon JP, Davies G Proc Natl Acad Sci U S A (1995) 92 (15): 7090-7094

Structural comparisons lead to the definition of a new superfamily of NAD(P)(H)-accepting oxidoreductases: the single-domain reductases/epimerases/dehydrogenases (the 'RED' family).Labesse G, Vidal-Cros A, Chomilier J, Gaudry M, Mornon JP Biochem J (1994) 304 : 95-99

Common prevalence of alanine and glycine in mobile reactive centre loops of serpins and viral fusion peptides: do prions possess a fusion peptide? Callebaut I, Tasso A, Brasseur R, Burny A, Portetelle D, Mornon JP J Comput Aided Mol Des (1994) 8:175-191

Identification of functional sites on bovine leukemia virus envelope glycoproteins using structural and immunological data. Callebaut I, Portetelle D, Burny A, Mornon JP Eur J Biochem (1994) 222: 405-414

The LW blood group glycoprotein is homologous to intercellular adhesion molecules. Bailly P, Hermand P, Callebaut I, Sonneborn HH, Khamlichi S, Mornon JP, Cartron JP Proc Natl Acad Sci U S A (1994) 91 (12): 5306-5310

An immunophilin that binds M(r) 90,000 heat shock protein: main structural features of a mammalian p59 protein. Callebaut I, Renoir JM, Lebeau MC, Massol N, Burny A, Baulieu EE, Mornon JP. Proc Natl Acad Sci U S A (1992) 89: 6270-6274

Molecular cloning and characterization of MPL, the human homolog of the v-mpl oncogene: identification of a member of the hematopoietic growth factor receptor superfamily.Vigon I, Mornon JP, Cocault L, Mitjavila MT, Tambourin P, Gisselbrecht S, Souyri M Proc Natl Acad Sci U S A (1992) 89 (12): 5640-5644

Main structural and functional features of the basic cytosolic bovine 21 kDa protein delineated through hydrophobic cluster analysis and molecular modelling. Schoentgen F, Seddiqi N, Bucquoy S, Jolles P, Lemesle-Varloot L, Provost K, Mornon JP Protein Eng (1992) 5 (4): 295-303

Structural symmetry of the extracellular domain of the cytokine/growth hormone/prolactin receptor family and interferon receptors revealed by hydrophobic cluster analysis. Thoreau E, Petridou B, Kelly PA, Djiane J, Mornon JP FEBS Lett (1991) 282 (1): 26-31

Cellulase families revealed by hydrophobic cluster analysis. Henrissat B, Claeyssens M, Tomme P, Lemesle L, Mornon JP Gene (1989) 81 (1): 83-95

Other sequence /structure analysis/modeling tools

New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. Wojcik J, Mornon JP, Chomilier J J Mol Biol (1999) 289(5):1469-90

Visual BLAST and Visual FASTA : graphic workbenches for interactive analysis of full BLAST and FASTA outputs under Microsoft Windows 95/NT. Durand P., Canard L. , Mornon J.P. (1997) Comput. Appl. Biosci. (1997) 13(4):407-413

P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins. Labesse G, Colloc'h N, Pothier J, Mornon JP Comput Appl Biosci (1997)13 (3): 291-295

MulBlast 1.0: a multiple alignment of BLAST output to boost protein sequence similarity analysis. Labesse G Comput Appl Biosci (1996) 12 (6): 463-467

Automat and BLAST: comparison of two protein sequence similarity search programs. Cantalloube H, Labesse G, Chomilier J, Nahum C, Cho YY, Chams V, Achour A, Lachgar A, Mbika JP, Issing W, et al Comput Appl Biosci (1995) 11 (3): 261-272

Automat: a novel software system for the systematic search for protein (or DNA) similarities with a notable application to autoimmune diseases and AIDS.Cantalloube H, Nahum C, Achour A, Lehner T, Callebaut I, Burny A, Bizzini B, Mornon JP, Zagury D, Zagury JF Comput Appl Biosci (1994) 10 (2): 153-161

Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon JP Protein Eng (1993) 6 (4): 377-382

FORME: an interactive package for protein backbone deformation.Tuffery P, Vaney MC, Mornon JP, Hazout S J Mol Graph (1991) 9 (3): 175-181

A new tool for the qualitative and quantitative analysis of protein surfaces using B-spline and density of surface neighborhood. Colloc'h N, Mornon JP J Mol Graph (1990) 8 (3): 133-140

Protein folding


Predicting the protein folding nucleus from a sequence. Poupon A, Mornon JP FEBS Lett (1999) 452(3):283-9

"Topohydrophobic positions" as key markers of globular protein folds. Poupon A, Mornon JP Theor. Chem. Accounts (1999) 101:2-8.

Populations of hydrophobic amino qcids within protein globular domains: identification of conserved "topohydrophobic" positions. Poupon A, Mornon JP Proteins (1998) 33(3):329-42

A global taxonomy of loops in globular proteins. Kwasigroch JM, Chomilier J, Mornon JP J Mol Biol (1996) 259 (4): 855-872

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