PFRMAT AL 
TARGET T0077 
AUTHOR 6180-8572-6816 
REMARK ---------------------------------------------------------------------------------- 
METHOD In general, all our predicitons were made with a combination of sequence 
METHOD searches and structure predictions, followed by extensive human 
METHOD interpretation of the results. The graphical representation of the combined 
METHOD results of different methods has been essential for the expert analysis of 
METHOD the predictions. 
METHOD  
METHOD For the sequence analysis the Genequiz server (Casari, 1996; Scharf, 1994) 
METHOD has been one of the primary sources of information. In depth analysis of 
METHOD different families were carried out with profile methods like HMM (Krogh, 1994). 
METHOD  
METHOD The structural analysis was supported by a new  graphical interface (Pazos 
METHOD et al., in preparation) for analysing the results of the TOPITS threading 
METHOD server (Rost, 1995). The interface includes the evaluation of other 
METHOD features like secondary structure and accessibility predictions (PHD 
METHOD server, Rost et al., 1993) , correlated mutations analysis (Gbel et al., 
METHOD 1994; Olmea and Valencia, 1997, Pazos et al., 1997a), tree-determinant 
METHOD analysis (Casari, 1995, Pazos et al., 1997b ), calculation and 
METHOD representation of conserved and conserved active site residues (Ouzounis et 
METHOD al., 1977). Links to the FSSP ( Holm and Sander, 1994 ) and Scop (Murzin, 1995) 
METHOD protein structure classification databases and to Medline  are 
METHOD facilitated. The visualisation of the different sequence features together 
METHOD with the sequence-structure alignments and the direct access to the 3D 
METHOD structures of the implicit models was done via a Rasmol (Sayle, 1995) interface. 
METHOD  
METHOD We have used a similar hybrid approach in previous  prediction exercises 
METHOD (Valencia et al., 1995, Pons et al., 1998a,b). 
METHOD  
METHOD ------ 
METHOD Casari G Sander, C., Valencia, A. (1995)  A method to predict functional 
METHOD residues in proteins. Nature Structural Biology 2: 171-178 
METHOD  
METHOD Casari G Ouzounis, C., Valencia, A.,  Sander, C. (1996). GeneQuiz II: 
METHOD automatic function assignment for genome sequence analysis. In L. Hunter 
METHOD (Ed.), Proceedings of the First Annual Pacific Symposium on Biocomputing, 
METHOD (pp. 707-709). Hawaii, USA: World Scientific. 
METHOD  
METHOD Gbel U, Sander C, Schneider R, Valencia A (1994) Correlated mutations and 
METHOD residue contacts in proteins. Proteins  18: 309-317 
METHOD  
METHOD Holm L,  Sander C (1994) The FSSP database of structurally aligned protein 
METHOD fold families. Nucl. Acids Res. 22: 3600-3609 
METHOD  
METHOD Olmea O,  Valencia A (1997) Improving contact predictions by the 
METHOD combination of correlated mutations and other sources of sequence 
METHOD information. Folding & Design 2: S25-S32 
METHOD  
METHOD Ouzounis, C., Perez-Irratxeta, C., Sander, C., Valencia, A. (1998) Are 
METHOD binding residues conserved?  In Proceedings of the Fifth Annual Pacific 
METHOD Symposium on Biocomputing. Hawaii, USA - World Scientific. 
METHOD  
METHOD Pazos F, Olmea O, Valencia A (1997a) A graphical interface for correlated 
METHOD mutations and other structure prediction methods. CABIOS 13: 319-321 
METHOD  
METHOD Pazos F, Sanchez-Pulido L, Garca-Ranea JA, Andrade MA, Atrian S, Valencia 
METHOD A (1997b). Comparative analysis of different methods for the detection of 
METHOD specificity regions in protein families. In D. Lundh Olsson, B., Narayanan 
METHOD A. (Eds.), Biocomputing and Emergent Computation (pp. 132-145). Singapore, 
METHOD New Jersey, London, Hong Kong: World Scientific. 
METHOD  
METHOD Pons, T., Chinea, G., Olmea, G., Beldarrain, A., Roca, H., Padron, G., 
METHOD Valencia, A. (1998) Structure prediction of the DEX extracellular 
METHOD dextranase. Proteins in the press. 
METHOD  
METHOD Pons, T.,  Olmea, O.,  Chinea, G., Beldarrain, A.,  Marquez, G., Acosta, 
METHOD N., Rodriguez, L.,Valencia, A. (1998) Structural model for family 32 of 
METHOD glycosyl-hydrolase enzymes. Proteins in the press. 
METHOD  
METHOD Rost B, Sander C, Schneider R (1994) PHD - an automatic mail server for 
METHOD protein secondary structure prediction. CABIOS 1994 Feb; 10(1): 53-60.  
METHOD  
METHOD Rost B (1995). TOPITS: Threading one dimensional predictions into three 
METHOD dimensional structures. In C. Rawlings & e. als (Ed.), Third International 
METHOD Conference on Intelligent Systems for Molecular Biology,  (pp. 314-321). 
METHOD England, Menlo Park: 
METHOD  
METHOD Scharf M Schneider, R., Casari, G., Bork, P., Valencia, A., Ouzounis, C., 
METHOD Sander, C. (1994) Genequiz: A workbench for sequence analysis. ISMB 1994: 
METHOD 384-353 
METHOD  
METHOD Valencia, A., Hubbard, T.J., Muga, A., Bauelos, S., Llorca, O., 
METHOD Carrascosa, J.L., Valpuesta, J.M. (1995)  Prediction of the structure of 
METHOD GroES and its interaction with GroEL. Proteins 22: 199-209. 
METHOD  
METHOD Krogh et al (94). J. Mol. Biol. 235:1501 
METHOD  
METHOD Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. "scop: a structural  
METHOD classification of proteins database for the investigation of sequences and  
METHOD structures" Journal of Molecular Biology 247:536-540.  
METHOD  
METHOD Sayle RA, et al. (1995). RASMOL: biomolecular graphics for all.  
METHOD Trends Biochem Sci. 1995 Sep; 20(9): 374. 
METHOD  
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MODEL  1 
PARENT NONE 
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