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Bibliography

Abagyan et al., 1994
Abagyan, R., Frishman, D. & Argos, P. (1994).
Recognition of distantly related proteins through energy calculations. Proteins: Struct., Funct., Genet. 19, 132-140.

Abrahams et al., 1994
Abrahams, J. P., Leslie, A. G. W., Lutter, R. & Walker, J. E. (1994).
Structure at 2.8Å resolution of F1-ATPase from bovine heart mitochondria. Nature 370, 621-628.

Altschul et al., 1990
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990).
Basic local alignment search tool. J. Mol. Biol. 215, 403-410.

Anfinsen, 1973
Anfinsen, C. B. (1973).
Principles that govern the folding of protein chains. Science 181, 223-230.

Arevalo et al., 1994
Arevalo, J. H., Hassig, C. A., Stura, E. A., Sims, M. J., Taussig, M. J. & Wilson, I. A. (1994).
Structural-analysis of antibody specificity -- detailed comparison of 5 Fab'-steroid complexes. J. Mol. Biol. 241, 663-690.

Argos, 1987
Argos, P. (1987).
A sensitive procedure to compare amino-acid sequences. J. Mol. Biol. 193, 385-396.

Argos et al., 1983
Argos, P., Hanei, M., Wilson, J. M. & Kelley, W. N. (1983).
A possible nucleotide-binding domain in the tertiary fold of phosphoribosyltransferases. J. Biol. Chem. 258, 6450- 6457.

Attwood et al., 1997
Attwood, T. K., Beck, M. E., Bleasby, A. J., Degtyarenko, K., Michie, A. D. & Parrysmith, D. J. (1997).
Novel developments with the PRINTS protein fingerprint database. Nuc. Ac. Res. 25, 212-216.

Aurora et al., 1994
Aurora, R., Srinivasan, R. & Rose, G. D. (1994).
Rules for alpha-helix termination by glycine. Science 264, 1126-1130.

Bailey, 1981
Bailey, N. T. J., (1981).
Statistical Methods in Biology.
Hodder and Stoughton, 2nd edition.

Bairoch & Apweller, 1997
Bairoch, A. & Apweller, R. (1997).
The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nuc. Ac. Res. 25, 31-36.

Bairoch & Boeckmann, 1991
Bairoch, A. & Boeckmann, B. (1991).
The SWISS-PROT protein-sequence data-bank. Nuc. Ac. Res. 19, 2247-2248.

Bairoch et al., 1997
Bairoch, A., Bucher, P. & Hofmann, K. (1997).
The PROSITE database, its status in 1997. Nuc. Ac. Res. 25, 217-221.

Bamborough & Cohen, 1996
Bamborough, P. & Cohen, F. E. (1996).
Modeling protein-ligand complexes. Curr. Opin. Struct. Biol. 6, 236-241.

Barker & Dayhoff, 1972
Barker, W. C. & Dayhoff, M. O., (1972).
Detecting distant relationships: Computer methods and results.
In Atlas of Protein Sequence and Structure (Dayhoff, M. O., ed.), volume 5. National Biomedical Research Foundation, Sliver Spring, Maryland.

Barlow & Richards, 1995
Barlow, T. W. & Richards, W. G. (1995).
A novel representation of protein-structure. J. Mol. Graph. 13, 373.

Barton, 1990
Barton, G. J. (1990).
Protein multiple sequence alignment and flexible pattern- matching. Meth. Enzymol. 183, 403-428.

Barton, 1995
Barton, G. J. (1995).
Protein secondary structure prediction. Curr. Opin. Struct. Biol. 5, 372-376.

Barton & Sternberg, 1987
Barton, G. J. & Sternberg, M. J. E. (1987).
Evaluation and improvements in the automatic alignment of protein sequences. Protein Eng. 1, 89-94.

Baumann et al., 1993
Baumann, U., Wu, S., Flaherty, K. M. & McKay, D. B. (1993).
3-dimensional structure of the alkaline protease of Pseudomonas aeruginosa -- a 2-domain protein with a calcium-binding parallel-beta roll motif. EMBO J. 12, 3357-3364.

Benner et al., 1994
Benner, S. A., Badcoe, I., Cohen, M. A. & Gerloff, D. L. (1994).
Bona-fide prediction of aspects of protein conformation -- assigning interior and surface residues from patterns of variation and conservation in homologous protein sequences. J. Mol. Biol. 235, 926-958.

Benner & Gerloff, 1991
Benner, S. A. & Gerloff, D. (1991).
Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure -- a prediction of the structure of the catalytic domain of protein-kinases. Adv. Enz. Reg. 31, 121-181.

Bernstein et al., 1977
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977).
The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.

Blundell & Johnson, 1993
Blundell, T. L. & Johnson, M. S. (1993).
Catching a common fold. Prot. Sci. 2, 877-883.

Boberg et al., 1995
Boberg, J., Salakoski, T. & Vihinen, M. (1995).
Accurate prediction of protein secondary structural class with fuzzy structural vectors. Protein Eng. 8, 505-512.

Bowie et al., 1990
Bowie, J. U., Clarke, N. D., Pabo, C. O. & Sauer, R. T. (1990).
Identification of protein folds -- matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins: Struct., Funct., Genet. 7, 257-264.

Bowie et al., 1991
Bowie, J. U., Luthy, R. & Eisenberg, D. (1991).
A method to identify protein sequences that fold into a known 3-dimensional structure. Science 253, 164-170.

Branden & Tooze, 1991
Branden, C. & Tooze, J., (1991).
Introduction to Protein Structure.
Garland Publishing, Inc., New York.

Brenner, 1996
Brenner, S. E., (1996).
Molecular propinquity: evolutionary and structural relationships of proteins.
PhD thesis, University of Cambridge.

Brinkman et al., 1990
Brinkman, K., Termaat, R., Berden, J. H. M. & Smeenk, R. J. T. (1990).
Anti-DNA antibodies and lupus nephritis: The complexity of cross-reactivity. Immun. Today 11, 232-234.

Brunger et al., 1991
Brunger, A. T., Leahy, D. J., Hynes, T. R. & Fox, R. O. (1991).
2.9 Å-resolution structure of an anti-dinitrophenyl-spin-label monoclonal-antibody Fab fragment with bound hapten. J. Mol. Biol. 221, 239-256.

Bruns & Karplus, 1995
Bruns, C. M. & Karplus, P. A. (1995).
Refined crystal-structure of spinach ferredoxin reductase at 1.7Å resolution -- oxidized, reduced and 2'-phospho-5'- AMP bound-states. J. Mol. Biol. 247, 125-145.

Bryant & Altschul, 1995
Bryant, S. H. & Altschul, S. F. (1995).
Statistics of sequence-structure threading. Curr. Opin. Struct. Biol. 5, 236-244.

Bull & Breese, 1974
Bull, H. & Breese, K. (1974).
Surface tension of amino acid solutions: A hydrophobicity scale of the amino acid residues. Arch. Biochem. Biophys. 161, 665-670.

Bult et al., 1996
Bult, C. J., White, O., Olsen, G. J., Zhou, L. X., Fleischmann, R. D., Sutton, G. G., Blake, J. A., Fitzgerald, L. M., Clayton, R. A., Gocayne, J. D., Kerlavage, A. R., Dougherty, B. A., Tomb, J. F., Adams, M. D., Reich, C. I., Overbeek, R., Kirkness, E. F., Weinstock, K. G., Merrick, J. M., Glodek, A., Scott, J. L., Geoghagen, N. S. M., Weidman, J. F., Fuhrmann, J. L., Nguyen, D., Utterback, T. R., Kelley, J. M., Peterson, J. D., Sadow, P. W., Hanna, M. C., Cotton, M. D., Roberts, K. M., Hurst, M. A., Kaine, B. P., Borodovsky, M., Klenk, H. P., Fraser, C. M., Smith, H. O., Woese, C. R. & Venter, J. C. (1996).
Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073.

Cabral et al., 1996
Cabral, J. H. M., Petosa, C., Sutcliffe, M. J., Raza, S., Byron, O., Poy, F., Marfatia, S. M., Chishti, A. H. & Liddington, R. C. (1996).
Crystal-structure of a PDZ domain. Nature 382, 649-652.

Carrington & Boothroyd, 1996
Carrington, M. & Boothroyd, J. (1996).
Implications of conserved structural motifs in disparate trypanosome surface-proteins. Mol. Biochem. Parasitol. 81, 119-126.

Cedano et al., 1997
Cedano, J., Aloy, P., Perezpons, J. A. & Querol, E. (1997).
Relation between amino acid composition and cellular location of proteins. J. Mol. Biol. 266, 594-600.

Chester & Hawkins, 1995
Chester, K. A. & Hawkins, R. E. (1995).
Clinical issues in antibody design. Trends Biotechnol. 13, 294-300.

Chothia, 1976
Chothia, C. (1976).
The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105, 1-14.

Chothia, 1992
Chothia, C. (1992).
Proteins -- 1000 families for the molecular biologist. Nature 357, 543-544.

Chothia & Janin, 1975
Chothia, C. & Janin, J. (1975).
Principles of protein-protein recognition. Nature 256, 705-708.

Chothia & Lesk, 1986
Chothia, C. & Lesk, A. M. (1986).
The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823-826.

Chothia & Lesk, 1987
Chothia, C. & Lesk, A. M. (1987).
Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901-917.

Chothia et al., 1986
Chothia, C., Lesk, A. M., Levitt, M., Amit, A. G., Mariuzza, R. A., Phillips, S. E. V. & Poljak, R. J. (1986).
The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure. Science 233, 755-758.

Chothia et al., 1989
Chothia, C., Lesk, A. M., Tramontano, A., Levitt, M., Smith-Gill, S. J., Air, G., Sheriff, S., Padlan, E. A., Davies, D. R., Tulip, W. R., Colman, P. M., Alzri, P. M. & Poljak, R. J. (1989).
Conformations of immunoglobulin hypervariable regions. Nature 342, 877-883.

Chou & Zhang, 1994
Chou, K. C. & Zhang, C. T. (1994).
Predicting protein-folding types by distance functions that make allowances for amino-acid interactions. J. Biol. Chem. 269, 22014-22020.

Chou & Zhang, 1995
Chou, K. C. & Zhang, C. T. (1995).
Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol. 30, 275-349.

Chou, 1989
Chou, P. Y., (1989).
Prediction of protein structural classes from amino acid composition.
In Prediction of protein structures and the principles of protein conformation (Fasman, G. D., ed.), pp. 549-586. Plenum Press.

Chou & Fasman, 1974
Chou, P. Y. & Fasman, G. D. (1974).
Prediction of protein conformation. Biochemistry 13, 222-245.

Churchill et al., 1994
Churchill, M. E. A., Stura, E. A., Pinilla, C., Appel, J. R., Houghten, R. A., Kono, D. H., Balderas, R. S., Fieser, G. G., Schulzegahmen, U. & Wilson, I. A. (1994).
Crystal-structure of a peptide complex of antiinfluenza peptide antibody-Fab-26/9 -- comparison of 2 different antibodies bound to the same peptide antigen. J. Mol. Biol. 241, 534-556.

Connolly, 1983
Connolly, M. L. (1983).
Analytical molecular surface calculation. J. Appl. Cryst. 16, 548-558.

Connolly, 1996
Connolly, M. L. (1996).
Molecular surfaces: A review. Network Science 2, http://www.awod.com/netsci/Science/Compchem/feature14.html.

Cook et al., 1992
Cook, W. J., Jeffrey, L. C., Sullivan, M. L. & Vierstra, R. D. (1992).
3-dimensional structure of a ubiquitin-conjugating enzyme (E2). J. Biol. Chem. 267, 15116-15121.

Cowan et al., 1992
Cowan, S. W., Schirmer, T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R. A., Jansonius, J. N. & Rosenbusch, J. P. (1992).
Crystal-structures explain functional-properties of 2 Escherichia coli porins. Nature 358, 727-733.

Dayhoff et al., 1978
Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C., (1978).
A model of evolutionary change in proteins.
In Atlas of Protein Sequence and Structure (Dayhoff, M. O., ed.), volume 5, Suppl. 3, pp. 345-352. National Biomedical Research Foundation, Silver Spring, Washington D.C.

Defay & Cohen, 1996
Defay, T. R. & Cohen, F. E. (1996).
Multiple sequence information for threading algorithms. J. Mol. Biol. 262, 314-323.

Deisenhofer et al., 1985
Deisenhofer, J., Epp, O., Miki, K., Huber, R. & Michel, H. (1985).
Structure of the protein subunits in the photosynthetic reaction center of Rhodopseudomonas viridis at 3Å resolution. Nature 318, 618-624.

Delaney, 1992
Delaney, J. S. (1992).
Finding and filling protein cavities using cellular logic operations. J. Mol. Graph. 10, 174.

Diederichs et al., 1991
Diederichs, K., Boone, T. & Karplus, P. A. (1991).
Novel fold and putative receptor-binding site of granulocyte-macrophage colony-stimulating factor. Science 254, 1779-1782.

Dill, 1990
Dill, K. A. (1990).
Dominant forces in protein folding. Biochemistry 29, 7133-7155.

Dill et al., 1995
Dill, K. A., Bromberg, S., Yue, K. Z., Fiebig, K. M., Yee, D. P., Thomas, P. D. & Chan, H. S. (1995).
Principles of protein-folding -- a perspective from simple exact models. Prot. Sci. 4, 561-602.

Donnelly et al., 1994
Donnelly, D., Overington, J. P. & Blundell, T. L. (1994).
The prediction and orientation of alpha-helices from sequence alignments -- the combined use of environment-dependent substitution tables, Fourier-transform methods and helix capping rules. Protein Eng. 7, 645-653.

Doolittle, 1981
Doolittle, R. F. (1981).
Similar amino-acid sequences -- chance or common ancestry? Science 214, 149-159.

Dubchak et al., 1995
Dubchak, I., Muchnik, I., Holbrook, S. R. & Kim, S. H. (1995).
Prediction of protein-folding class using global description of amino-acid-sequence. Proc. Natl. Acad. Sci. USA 92, 8700-8704.

Dunbrack et al., 1997
Dunbrack, R. L., Gerloff, D. L., Bower, M., Chen, X. W., Lichtarge, O. & Cohen, F. E. (1997).
Meeting review: the second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar, California, December 13-16, 1996. Folding & Design 2, R27-R42.

Durbin & Mitchison, 1990
Durbin, R. & Mitchison, G. (1990).
A dimension reduction framework for understanding cortical maps. Nature 343, 644-647.

Eddy, 1996
Eddy, S. R. (1996).
Hidden Markov-models. Curr. Opin. Struct. Biol. 6, 361-365.

Eisenberg & McLachlan, 1986
Eisenberg, D. & McLachlan, A. D. (1986).
Solvation energy in protein folding and binding. Nature 319, 199-203.

Eisenhaber et al., 1996b
Eisenhaber, F., Frommel, C. & Argos, P. (1996b).
Prediction of secondary structural content of proteins from their amino-acid-composition alone. (2) The paradox with secondary structural class. Proteins: Struct., Funct., Genet. 25, 169-179.

Eisenhaber et al., 1996a
Eisenhaber, F., Imperiale, F., Argos, P. & Frommel, C. (1996a).
Prediction of secondary structural content of proteins from their amino-acid-composition alone. (1) New analytic vector decomposition methods. Proteins: Struct., Funct., Genet. 25, 157-168.

Elmasry & Fersht, 1994
Elmasry, N. F. & Fersht, A. R. (1994).
Mutational analysis of the N-capping box of the alpha-helix of chymotrypsin inhibitor-2. Protein Eng. 7, 777-782.

Falicov & Cohen, 1996
Falicov, A. & Cohen, F. E. (1996).
A surface of minimum area metric for the structural comparison of proteins. J. Mol. Biol. 258, 871-892.

Farber, 1993
Farber, G. K. (1993).
An alpha/beta-barrel full of evolutionary trouble. Curr. Opin. Struct. Biol. 3, 409-412.

Ferran et al., 1994
Ferran, E. A., Pflugfelder, B. & Ferrara, P. (1994).
Self-organized neural maps of human protein sequences. Prot. Sci. 3, 507-521.

Fersht, 1984
Fersht, A. R. (1984).
Basis of biological specificity. Trends Biochem. Sci. 9, 145-147.

Fersht, 1987
Fersht, A. R. (1987).
The hydrogen-bond in molecular recognition. Trends Biochem. Sci. 12, 301-304.

Fischer & Eisenberg, 1996
Fischer, D. & Eisenberg, D. (1996).
Protein fold recognition using sequence-derived predictions. Prot. Sci. 5, 947-955.

Fischer et al., 1996
Fischer, D., Elofsson, A., Rice, D. & Eisenberg, D., (1996).
Assessing the performance of fold recognition methods by means of a comprehensive benchmark.
In Pacific Symposium on Biocomputing, Hawaii., pp. 300-318.

Fiser et al., 1996
Fiser, A., Simon, I. & Barton, G. J. (1996).
Conservation of amino-acids in multiple alignments -- aspartic acid has unexpected conservation. FEBS Lett. 397, 225-229.

Fleischmann et al., 1995
Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J. F., Dougherty, B. A., Merrick, J. M., McKenney, K., Sutton, G., Fitzhugh, W., Fields, C., Gocayne, J. D., Scott, J., Shirley, R., Liu, L. I., Glodek, A., Kelley, J. M., Weidman, J. F., Phillips, C. A., Spriggs, T., Hedblom, E., Cotton, M. D., Utterback, T. R., Hanna, M. C., Nguyen, D. T., Saudek, D. M., Brandon, R. C., Fine, L. D., Fritchman, J. L., Fuhrmann, J. L., Geoghagen, N. S. M., Gnehm, C. L., McDonald, L. A., Small, K. V., Fraser, C. M., Smith, H. O. & Venter, J. C. (1995).
Whole-genome random sequencing and assembly of Haemophilus influenzae rd. Science 269, 496-512.

Flockner et al., 1995
Flockner, H., Braxenthaler, M., Lackner, P., Jaritz, M., Ortner, M. & Sippl, M. J. (1995).
Progress in fold recognition. Proteins: Struct., Funct., Genet. 23, 376-386.

Flores et al., 1994
Flores, T. P., Moss, D. S. & Thornton, J. M. (1994).
An algorithm for automatically generating protein topology cartoons. Protein Eng. 7, 31-37.

Fraser et al., 1995
Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., Fritchman, J. L., Weidman, J. F., Small, K. V., Sandusky, M., Fuhrmann, J., Nguyen, D., Utterback, T. R., Saudek, D. M., Phillips, C. A., Merrick, J. M., Tomb, J. F., Dougherty, B. A., Bott, K. F., Hu, P. C., Lucier, T. S., Peterson, S. N., Smith, H. O., Hutchison, C. A. & Venter, J. C. (1995).
The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403.

Freedman, 1995
Freedman, R. B. (1995).
The formation of protein disulfide bonds. Curr. Opin. Struct. Biol. 5, 85-91.

Frishman & Argos, 1996
Frishman, D. & Argos, P. (1996).
Incorporation of non-local interactions in protein secondary structure prediction from the amino-acid sequence. Protein Engineering 9, 133-142.

Frishman & Argos, 1997a
Frishman, D. & Argos, P. (1997a).
The future of protein secondary structure prediction accuracy. Folding & Design 2, 159-162.

Frishman & Argos, 1997b
Frishman, D. & Argos, P. (1997b).
Seventy-five percent accuracy in protein secondary structure prediction. Proteins: Struct., Funct., Genet. 27, 329-335.

Garnier et al., 1978
Garnier, J., Osguthorpe, D. J. & Robson, B. (1978).
Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 120, 97-120.

Gerstein, 1992
Gerstein, M. (1992).
A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen combining sites. Acta Cryst. A48, 271-276.

Gibrat et al., 1987
Gibrat, J. F., Garnier, J. & Robson, B. (1987).
Further developments of protein secondary structure prediction using information-theory -- new parameters and consideration of residue pairs. J. Mol. Biol. 198, 425-443.

Gobel et al., 1994
Gobel, U., Sander, C., Schneider, R. & Valencia, A. (1994).
Correlated mutations and residue contacts in proteins. Proteins: Struct., Funct., Genet. 18, 309-317.

Godzik et al., 1992
Godzik, A., Kolinski, A. & Skolnick, J. (1992).
Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol. 227, 227-238.

Gribskov et al., 1990
Gribskov, M., Luthy, R. & Eisenberg, D. (1990).
Profile analysis. Meth. Enzymol. 183, 146-159.

Gribskov et al., 1987
Gribskov, M., McLachlan, A. D. & Eisenberg, D. (1987).
Profile analysis -- detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84, 4355-4358.

Han & Baker, 1995
Han, K. F. & Baker, D. (1995).
Recurring local sequence motifs in proteins. J. Mol. Biol. 251, 176-187.

Han & Baker, 1996
Han, K. F. & Baker, D. (1996).
Global properties of the mapping between local amino-acid sequence and local-structure in proteins. Proc. Natl. Acad. Sci. USA 93, 5814-5818.

Hanke et al., 1996
Hanke, J., Beckmann, G., Bork, P. & Reich, J. G. (1996).
Self-organizing hierarchical networks for pattern-recognition in protein-sequence. Prot. Sci. 5, 72-82.

Hao et al., 1992
Hao, M. H., Rackovsky, S., Liwo, A., Pincus, M. R. & Scheraga, H. A. (1992).
Effects of compact volume and chain stiffness on the conformations of native proteins. Proc. Natl. Acad. Sci. USA 89, 6614-6618.

Hartl, 1996
Hartl, F. U. (1996).
Molecular chaperones in cellular protein-folding. Nature 381, 571-580.

Hendlich et al., 1990
Hendlich, M., Lackner, P., Weitckus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G. & Sippl, M. J. (1990).
Identification of native protein folds amongst a large number of incorrect models -- the calculation of low-energy conformations from potentials of mean force. J. Mol. Biol. 216, 167-180.

Henikoff, 1996
Henikoff, S. (1996).
Scores for sequence searches and alignments. Curr. Opin. Struct. Biol. 6, 353-360.

Henikoff & Henikoff, 1992
Henikoff, S. & Henikoff, J. G. (1992).
Amino-acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915-10919.

Henikoff & Henikoff, 1994
Henikoff, S. & Henikoff, J. G. (1994).
Protein family classification based on searching a database of blocks. Genomics 19, 97-107.

Henikoff & Henikoff, 1997
Henikoff, S. & Henikoff, J. G. (1997).
Embedding strategies for effective use of information from multiple sequence alignments. Prot. Sci. 6, 698-705.

Hennig et al., 1995
Hennig, M., Darimont, B., Sterner, R., Kirschner, K. & Jansonius, J. N. (1995).
2.0Å structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus -- possible determinants of protein stability. Structure 3, 1295-1306.

Herron et al., 1991
Herron, J. N., He, X. M., Ballard, D. W., Blier, P. R., Pace, P. E., Bothwell, A. L. M., Voss, E. W. & Edmundson, A. B. (1991).
An auto-antibody to single-stranded-DNA -- comparison of the 3-dimensional structures of the unliganded Fab and a deoxynucleotide Fab complex. Proteins: Struct., Funct., Genet. 11, 159-175.

Hilvert, 1994
Hilvert, D. (1994).
Catalytic antibodies. Curr. Opin. Struct. Biol. 4, 612-617.

Hobohm & Sander, 1995
Hobohm, U. & Sander, C. (1995).
A sequence property approach to searching protein databases. J. Mol. Biol. 251, 390-399.

Holm & Sander, 1993
Holm, L. & Sander, C. (1993).
Protein-structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.

Holm & Sander, 1994
Holm, L. & Sander, C. (1994).
The FSSP database of structurally aligned protein fold families. Nuc. Ac. Res. 22, 3600-3609.

Hubbard & Argos, 1994
Hubbard, S. J. & Argos, P. (1994).
Cavities and packing at protein interfaces. Prot. Sci. 3, 2194-2206.

Hubbard & Park, 1995
Hubbard, T. J. & Park, J. (1995).
Fold recognition and ab initio structure predictions using hidden Markov-models and beta-strand pair potentials. Proteins: Struct., Funct., Genet. 23, 398-402.

Hubbard, 1997
Hubbard, T. J. P. (1997).
New horizons in sequence analysis. Curr. Opin. Struct. Biol. 7, 190-193.

Hutchinson & Thornton, 1990
Hutchinson, E. G. & Thornton, J. M. (1990).
HERA -- a program to draw schematic diagrams of protein secondary structures. Proteins: Struct., Funct., Genet. 8, 203-212.

Hutchinson & Thornton, 1994
Hutchinson, E. G. & Thornton, J. M. (1994).
A revised set of potentials for beta-turn formation in proteins. Prot. Sci. 3, 2207-2216.

Islam et al., 1995
Islam, S. A., Luo, J. C. & Sternberg, M. J. E. (1995).
Identification and analysis of domains in proteins. Protein Eng. 8, 513-525.

Jeffrey et al., 1995
Jeffrey, P. D., Schildbach, J. F., Chang, C. Y. Y., Kussie, P. H., Margolies, M. N. & Sheriff, S. (1995).
Structure and specificity of the antidigoxin antibody-40-50. J. Mol. Biol. 248, 344-360.

Jimenez et al., 1994
Jimenez, M. A., Munoz, V., Rico, M. & Serrano, L. (1994).
Helix stop and start signals in peptides and proteins -- the capping box does not necessarily prevent helix elongation. J. Mol. Biol. 242, 487-496.

Johnson & Overington, 1993
Johnson, M. S. & Overington, J. P. (1993).
A structural basis for sequence comparisons -- an evaluation of scoring methodologies. J. Mol. Biol. 233, 716-738.

Johnson et al., 1990
Johnson, M. S., Sali, A. & Blundell, T. L. (1990).
Phylogenetic-relationships from 3-dimensional protein structures. Meth. Enzymol. 183, 670-690.

Jones et al., 1992
Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992).
A new approach to protein fold recognition. Nature 358, 86-89.

Jones & Thornton, 1996
Jones, D. T. & Thornton, J. M. (1996).
Potential-energy functions for threading. Curr. Opin. Struct. Biol. 6, 210-216.

Jones & Thornton, 1995
Jones, S. & Thornton, J. M. (1995).
Protein-protein interactions -- a review of protein dimer structures. Progr. Biophy. molec. Biol. 63, 31-65.

Jones & Thornton, 1996
Jones, S. & Thornton, J. M. (1996).
Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA 93, 13-20.

Kabsch & Sander, 1983
Kabsch, W. & Sander, C. (1983).
Dictionary of protein secondary structure -- pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.

Kabsch & Sander, 1984
Kabsch, W. & Sander, C. (1984).
On the use of sequence homologies to predict protein-structure -- identical pentapeptides can have completely different conformations. Proc. Natl. Acad. Sci. USA 81, 1075-1078.

Kendrew et al., 1958
Kendrew, J. C. et al. (1958).
A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181, 662-666.

Kendrew et al., 1960
Kendrew, J. C. et al. (1960).
Structure of myoglobin. Nature 185, 422-427.

Killard et al., 1995
Killard, A. J., Deasy, B., O'Kennedy, R. & Smyth, M. R. (1995).
Antibodies -- production, functions and applications in biosensors. Trends Anal. Chem. 14, 257-266.

King & Sternberg, 1996
King, R. D. & Sternberg, M. J. E. (1996).
Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Prot. Sci. 5, 2298-2310.

Klein & Schulz, 1991
Klein, C. & Schulz, G. E. (1991).
Structure of cyclodextrin glycosyltransferase refined at 2.0-Å resolution. J. Mol. Biol. 217, 737-750.

Klein & Delisi, 1986a
Klein, P. & Delisi, C. (1986a).
Prediction of protein structural class from the amino-acid sequence. Biopolymers 25, 1659-1672.

Klein & Delisi, 1986b
Klein, P. & Delisi, C. (1986b).
Prediction of protein structural class from the amino-acid sequence. Biopolymers 25, 1659-1672.

Kohonen, 1990
Kohonen, T. (1990).
The self-organizing map. Proc. IEEE 78, 1464-1480.

Kohonen, 1993
Kohonen, T. (1993).
Physiological interpretation of the self-organizing map algorithm. Neur. Networks 6, 895-905.

Kohonen & Makisara, 1989
Kohonen, T. & Makisara, K. (1989).
The self-organizing feature maps. Phys. Scripta 39, 168-172.

Korndorfer et al., 1995
Korndorfer, I., Steipe, B., Huber, R., Tomschy, A. & Jaenicke, R. (1995).
The crystal-structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5Å resolution. J. Mol. Biol. 246, 511-521.

Kraulis, 1991
Kraulis, P. J. (1991).
Molscript -- a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.

Krogh et al., 1994
Krogh, A., Brown, M., Mian, I. S., Sjolander, K. & Haussler, D. (1994).
Hidden Markov-models in computational biology -- applications to protein modeling. J. Mol. Biol. 235, 1501-1531.

Kubota et al., 1981
Kubota, Y., Takahashi, S., Nishikawa, K. & Ooi, T. (1981).
Homology in protein sequences expressed by correlation- coefficients. J. Theor. Biol. 91, 347-361.

Kuhn et al., 1992
Kuhn, L. A., Siani, M. A., Pique, M. E., Fisher, C. L., Getzoff, E. D. & Tainer, J. A. (1992).
The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J. Mol. Biol. 228, 13-22.

Kyte & Doolittle, 1982
Kyte, J. & Doolittle, R. F. (1982).
A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.

Ladunga & Smith, 1997
Ladunga, I. & Smith, R. F. (1997).
Amino acid substitutions preserve protein folding by conserving steric and hydrophobicity properties. Protein Eng. 10, 187-196.

Laskowski et al., 1996
Laskowski, R. A., Luscombe, N. M., Swindells, M. B. & Thornton, J. M. (1996).
Protein clefts in molecular recognition and function. Prot. Sci. 5, 2438-2452.

Lathrop, 1994
Lathrop, R. H. (1994).
The protein threading problem with sequence amino-acid interaction preferences is NP-complete. Protein Eng. 7, 1059-1068.

Lathrop & Smith, 1996
Lathrop, R. H. & Smith, T. F. (1996).
Global optimum protein threading with gapped alignment and empirical pair score functions. J. Mol. Biol. 255, 641-665.

Lattman, 1995
Lattman, E. E. (1995).
Protein-structure prediction -- a special issue. Proteins: Struct., Funct., Genet. 23, 1.

Lawrence & Colman, 1993
Lawrence, M. C. & Colman, P. M. (1993).
Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946-950.

Lee & Richards, 1971
Lee, B. K. & Richards, F. M. (1971).
The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55, 379-400.

Lemer et al., 1995
Lemer, C. M. R., Rooman, M. J. & Wodak, S. J. (1995).
Protein-structure prediction by threading methods -- evaluation of current techniques. Proteins: Struct., Funct., Genet. 23, 337-355.

Lescar et al., 1995
Lescar, J., Pellegrini, M., Souchon, H., Tello, D., Poljak, R. J., Peterson, N., Greene, M. & Alzari, P. M. (1995).
Crystal-structure of a cross-reaction complex between Fab F9.13.7 and guinea-fowl lysozyme. J. Biol. Chem. 270, 18067-18076.

Levinthal, 1968
Levinthal, C. (1968).
Are there pathways for protein folding? J. Chem. Phys. 65, 44-45.

Levitt & Chothia, 1976
Levitt, M. & Chothia, C. (1976).
Structural patterns in globular proteins. Nature 261, 552-557.

Lim, 1974a
Lim, V. I. (1974a).
Structural principles of the globular organisation of protein chains. a stereochemical theory of globular protein secondary structure. J. Mol. Biol. 88, 857-872.

Lim, 1974b
Lim, V. I. (1974b).
Algorithms for the prediction of $\alpha $-helical and $\beta $-structural regions in globular proteins. J. Mol. Biol. 88, 873-894.

Love et al., 1993
Love, R. A., Villafranca, J. E., Aust, R. M., Nakamura, K. K., Jue, R. A., Major, J. G., Radhakrishnan, R. & Butler, W. F. (1993).
How the anti-(metal chelate) antibody CHA255 is specific for the metal-ion of its antigen -- X-ray structures for 2 Fab' hapten complexes with different metals in the chelate. Biochemistry 32, 10950-10959.

Low et al., 1968
Low, B. W., Lovell, F. W. & Rudko, A. D. (1968).
Prediction of alpha-helical regions in proteins of known sequence. Proc. Natl. Acad. Sci. USA 60, 1519-1526.

MacCallum et al., 1996
MacCallum, R. M., Martin, A. C. R. & Thornton, J. M. (1996).
Antibody-antigen interactions: Contact analysis and binding site topography. J. Mol. Biol. 262.5, 732-745.

Madej et al., 1995
Madej, T., Gibrat, J. F. & Bryant, S. H. (1995).
Threading a database of protein cores. Proteins: Struct., Funct., Genet. 23, 356-369.

Marchler-Bauer & Bryant, 1997
Marchler-Bauer, A. & Bryant, S. H. (1997).
A measure of success in fold recognition. Trends Biochem. Sci. 22, 236-240.

Martin & Thornton, 1996
Martin, A. C. R. & Thornton, J. M. (1996).
Structural families in loops of homologous proteins -- automatic classification, modeling and application to antibodies. J. Mol. Biol. 263, 800-815.

Martin et al., 1995
Martin, A. C. R., Toda, K., Stirk, H. J. & Thornton, J. M. (1995).
Long loops in proteins. Protein Eng. 8, 1093-1101.

Martin et al., 1991
Martin, A. C. R., Cheetham, J. C. & Rees, A. R. (1991).
Molecular modelling of antibody combining sites. Meth. Enzymol. 203, 121-153.

Matsuo & Nishikawa, 1995
Matsuo, Y. & Nishikawa, K. (1995).
Assessment of a protein fold recognition method that takes into account 4 physicochemical properties -- side-chain packing, solvation, hydrogen-bonding, and local conformation. Proteins: Struct., Funct., Genet. 23, 370-375.

Matthews, 1975
Matthews, B. W. (1975).
Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405, 442-451.

May, 1996
May, A. C. W. (1996).
Pairwise iterative superposition of distantly related proteins and assessment of the significance of 3-D structural similarity. Protein Eng. 9, 1093-1101.

May & Johnson, 1994
May, A. C. W. & Johnson, M. S. (1994).
Protein-structure comparisons using a combination of a genetic algorithm, dynamic-programming and least-squares minimization. Protein Eng. 7, 475-485.

May & Johnson, 1995
May, A. C. W. & Johnson, M. S. (1995).
Improved genetic algorithm-based protein-structure comparisons -- pairwise and multiple superpositions. Protein Eng. 8, 873-882.

McLachlan et al., 1984
McLachlan, A. D., Staden, R. & Boswell, D. R. (1984).
A method for measuring the non-random bias of a codon usage table. Nuc. Ac. Res. 12, 9567-9575.

Metfessel et al., 1993
Metfessel, B. A., Saurugger, P. N., Connelly, D. P. & Rich, S. S. (1993).
Cross-validation of protein structural class prediction using statistical clustering and neural networks. Prot. Sci. 2, 1171-1182.

Michie et al., 1996
Michie, A. D., Orengo, C. A. & Thornton, J. M. (1996).
Analysis of domain structural class using an automated class assignment protocol. J. Mol. Biol. 262, 168-185.

Michie et al., 1994
Michie, D., Spiegelhalter, D. J. & Taylor, C. C., (1994).
Machine learning, neural and statistical classification.
Ellis Horwood.

Miller, 1994
Miller, K. D. (1994).
Models of activity-dependent neural development. Prog. Brain Res. 102, 303-318.

Murzin et al., 1995
Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995).
SCOP -- a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.

Muskal & Kim, 1992
Muskal, S. M. & Kim, S. H. (1992).
Predicting protein secondary structure-content -- a tandem neural network approach. J. Mol. Biol. 225, 713-727.

Nagano, 1973
Nagano, K. (1973).
Logical analysis of the mechanism of protein folding. J. Mol. Biol. 75, 401-420.

Nakai et al., 1988
Nakai, K., Kidera, A. & Kanehisa, M. (1988).
Cluster-analysis of amino-acid indexes for prediction of protein- structure and function. Protein Eng. 2, 93-100.

Nakashima & Nishikawa, 1992
Nakashima, H. & Nishikawa, K. (1992).
The amino-acid-composition is different between the cytoplasmic and extracellular sides in membrane-proteins. FEBS Lett. 303, 141-146.

Nakashima & Nishikawa, 1994
Nakashima, H. & Nishikawa, K. (1994).
Discrimination of intracellular and extracellular proteins using amino-acid-composition and residue-pair frequencies. J. Mol. Biol. 238, 54-61.

Nakashima et al., 1986
Nakashima, H., Nishikawa, K. & Ooi, T. (1986).
The folding type of a protein is relevant to the amino-acid composition. J. Biochem. 99, 153-162.

NC-IUBMB, 1992
NC-IUBMB, (1992).
Enzyme Nomenclature.
Academic Press.

Needleman & Wunsch, 1970
Needleman, S. B. & Wunsch, C. D. (1970).
A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.

Nicholls et al., 1991
Nicholls, A., Sharp, K. A. & Honig, B. (1991).
Protein folding and association -- insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct., Funct., Genet. 11,, 281-296.

Nishikawa et al., 1983
Nishikawa, K., Kubota, Y. & Ooi, T. (1983).
Classification of proteins into groups based on amino-acid composition and other characters (2) Grouping into 4 types. J. Biochem. 94, 997-1007.

Nishikawa & Ooi, 1982
Nishikawa, K. & Ooi, T. (1982).
Correlation of the amino-acid composition of a protein to its structural and biological characters. J. Biochem. 91, 1821-1824.

Noble et al., 1993
Noble, M. E. M., Cleasby, A., Johnson, L. N., Egmond, M. R. & Frenken, L. G. J. (1993).
The crystal-structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate. FEBS Lett. 331, 123-128.

Noji et al., 1997
Noji, H., Yasuda, R., Yoshida, M. & Kinosita, K. (1997).
Direct observation of the rotation of F-1-ATPase. Nature 386, 299-302.

Norel et al., 1994
Norel, R., Lin, S. L., Wolfson, H. J. & Nussinov, R. (1994).
Shape complementarity at protein-protein interfaces. Biopolymers 34, 933-940.

Olmea & Valencia, 1997
Olmea, O. & Valencia, A. (1997).
Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Folding & Design 2, s25-s32.

Orengo et al., 1994
Orengo, C. A., Jones, D. T. & Thornton, J. M. (1994).
Protein superfamilies and domain superfolds. Nature 372, 631-634.

Orengo et al., 1997
Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. (1997).
A hierarchic classification of protein domain structures. Structure 5, 1093-1108.

Padlan et al., 1995
Padlan, E. A., Abergel, C. & Tipper, J. P. (1995).
Identification of specificity-determining residues in antibodies. FASEB J. 9, 133-139.

Padlan et al., 1989
Padlan, E. A., Silverton, E. W., Sheriff, S., Cohen, G. H., Smithgill, S. J. & Davies, D. R. (1989).
Structure of an antibody antigen complex -- crystal-structure of the HyHEL-10 Fab-lysozyme complex. Proc. Natl. Acad. Sci. USA 86, 5938-5942.

Pauling & Corey, 1951
Pauling, L. & Corey, R. B. (1951).
Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proc. Natl. Acad. Sci. USA 37, 729-740.

Pauling et al., 1951
Pauling, L., Corey, R. B. & Branson, H. R. (1951).
The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. USA 37, 205-211.

Pearson, 1990
Pearson, W. R. (1990).
Rapid and sensitive sequence comparison with FASTP and FASTA. Meth. Enzymol. 183, 63-98.

Pearson, 1995
Pearson, W. R. (1995).
Comparison of methods for searching protein-sequence databases. Prot. Sci. 4, 1145-1160.

Periti et al., 1967
Periti, P. F., Quagliarotti, G. & Liquori, A. M. (1967).
Recognition of alpha-helical segments in proteins of known primary structure. J. Mol. Biol. 24, 313-322.

Peters et al., 1996
Peters, K. P., Fauck, J. & Frommel, C. (1996).
The automatic search for ligand-binding sites in proteins of known 3-dimensional structure using only geometric criteria. J. Mol. Biol. 256, 201-213.

Phillips, 1970
Phillips, D. C. (1970).
Development of crystallographic enzymology. Biochem. Soc. Symp. 31, 11-28.

Pokkuluri et al., 1994
Pokkuluri, P. R., Bouthillier, F., Li, Y. G., Kuderova, A., Lee, J. & Cygler, M. (1994).
Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA -- crystal-structures of native Fab and 3 Fab-mononucleotide complexes. J. Mol. Biol. 243, 283-297.

Ponder & Richards, 1987
Ponder, J. W. & Richards, F. M. (1987).
Tertiary templates for proteins -- use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193, 775-791.

Prasad et al., 1988
Prasad, L., Vandonselaar, M., Lee, J. S. & Delbaere, L. T. J. (1988).
Structure determination of a monoclonal Fab fragment specific for histidine-containing protein of the phosphoenolpyruvate -- sugar phosphotransferase system of Escherichia coli. J. Biol. Chem. 263, 2571- 2574.

Presnell et al., 1992
Presnell, S. R., Cohen, B. I. & Cohen, F. E. (1992).
A segment-based approach to protein secondary structure prediction. Biochemistry 31, 983-993.

Ptitsyn, 1969
Ptitsyn, O. B. (1969).
Statistical analysis of the distribution of amino acid residues among helical and non-helical regions in globular proteins. J. Mol. Biol. 42, 501-510.

Radzicka & Wolfenden, 1988
Radzicka, A. & Wolfenden, R. (1988).
Comparing the polarities of the amino-acids -- side-chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous-solution. Biochemistry 27, 1664-1670.

Rao & G., 1973
Rao, S. T. & G., R. M. (1973).
Comparison of super-secondary structures in proteins. J. Mol. Biol. 286, 241-256.

Reardon & Farber, 1995
Reardon, D. & Farber, G. K. (1995).
Protein motifs (4) The structure and evolution of alpha/beta barrel proteins. FASEB J. 9, 497-503.

Rees et al., 1994
Rees, A. R., Staunton, D., Webster, D. M., Searle, S. J., Henry, A. H. & Pedersen, J. T. (1994).
Antibody design: beyond the natural limits. Trends Biotechnol. 12, 199-206.

Rice & Eisenberg, 1997
Rice, D. W. & Eisenberg, D. (1997).
A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J. Mol. Biol. 267, 1026-1038.

Richards, 1974
Richards, F. M. (1974).
The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1-14.

Richardson, 1981
Richardson, J. S. (1981).
The anatomy and taxonomy of protein structure. Adv. Prot. Chem. 34, 168-339.

Richardson, 1985
Richardson, J. S. (1985).
Schematic drawings of protein structures. Meth. Enzymol. 115, 359-380.

Richardson, 1986
Richardson, J. S. (1986).
Beta-sheet -- the greek key topology as a favored form in folding and structure. Federation Proceedings 45, 1829.

Rini et al., 1993
Rini, J. M., Stanfield, R. L., Stura, E. A., Salinas, P. A., Profy, A. T. & Wilson, I. A. (1993).
Crystal-structure of a human-immunodeficiency-virus type-1 neutralizing antibody, 50.1, in complex with its V3 loop peptide antigen. Proc. Natl. Acad. Sci. USA 90, 6325-6329.

Rohde & Bork, 1993
Rohde, K. & Bork, P. (1993).
A fast, sensitive pattern-matching approach for protein sequences. Comput. Appl. Biosci. 9, 183-189.

Rooman & Wodak, 1991
Rooman, M. J. & Wodak, S. J. (1991).
Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins. Proteins: Struct., Funct., Genet. 9, 69-78.

Rost et al., 1995
Rost, B., Casadio, R., Fariselli, P. & Sander, C. (1995).
Transmembrane helices predicted at 95-percent accuracy. Prot. Sci. 4, 521-533.

Rost & Sander, 1993
Rost, B. & Sander, C. (1993).
Prediction of protein secondary structure at better than 70 percent accuracy. J. Mol. Biol. 232, 584-599.

Rost & Sander, 1994
Rost, B. & Sander, C. (1994).
Combining evolutionary information and neural networks to predict protein secondary structure. Proteins: Struct., Funct., Genet. 19, 55-72.

Rost et al., 1994
Rost, B., Sander, C. & Schneider, R. (1994).
Redefining the goals of protein secondary structure prediction. J. Mol. Biol. 235, 13-26.

Rost et al., 1997
Rost, B., Schneider, R. & Sander, C. (1997).
Protein fold recognition by prediction-based threading. J. Mol. Biol. 270, 471-480.

Russell & Barton, 1992
Russell, R. B. & Barton, G. J. (1992).
Multiple protein-sequence alignment from tertiary structure comparison -- assignment of global and residue confidence levels. Proteins: Struct., Funct., Genet. 14, 309-323.

Russell & Barton, 1993
Russell, R. B. & Barton, G. J. (1993).
The limits of protein secondary structure prediction accuracy from multiple sequence alignment. J. Mol. Biol. 234, 951-957.

Russell & Barton, 1994
Russell, R. B. & Barton, G. J. (1994).
Structural features can be unconserved in proteins with similar folds -- an analysis of side-chain to side-chain contacts secondary structure and accessibility. J. Mol. Biol. 244, 332-350.

Russell et al., 1996
Russell, R. B., Copley, R. R. & Barton, G. J. (1996).
Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol. 259, 349-365.

Russell et al., 1997
Russell, R. B., Saqi, M. A. S., Sayle, R. A., Bates, P. A. & Sternberg, M. J. E. (1997).
Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation. J. Mol. Biol. 269, 423-439.

Sack et al., 1989
Sack, J. S., Saper, M. A. & Quiocho, F. A. (1989).
Periplasmic binding-protein structure and function -- refined X-ray structures of the leucine isoleucine valine-binding protein and its complex with leucine. J. Mol. Biol. 206, 171-191.

Salamov & Solovyev, 1995
Salamov, A. A. & Solovyev, V. V. (1995).
Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. J. Mol. Biol. 247, 11-15.

Salamov & Solovyev, 1997
Salamov, A. A. & Solovyev, V. V. (1997).
Protein secondary structure prediction using local alignments. J. Mol. Biol. 268, 31-36.

Sammon, 1969
Sammon, J. W. (1969).
A nonlinear mapping for data structure analysis. IEEE Trans. Comput. C-18, 401-409.

Sanchez & Sali, 1997
Sanchez, R. & Sali, A. (1997).
Advances in comparative protein-structure modelling. Curr. Opin. Struct. Biol. 7, 206-214.

Sander & Schneider, 1991
Sander, C. & Schneider, R. (1991).
Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Struct., Funct., Genet. 9, 56-68.

Satow et al., 1986
Satow, Y., Cohen, G. H., Padlan, E. A. & Davies, D. R. (1986).
Phosphocholine binding immunoglobulin Fab McPC603 an X-ray- diffraction study at 2.7Å. J. Mol. Biol. 190, 593-604.

Sayle & Milnerwhite, 1995
Sayle, R. A. & Milnerwhite, E. J. (1995).
Rasmol -- biomolecular graphics for all. Trends Biochem. Sci. 20, 374-376.

Schulz, 1977
Schulz, G. E. (1977).
Recognition of phylogenetic relationships from polypeptide chain fold similarities. J. Molec. Evol. 9, 339-342.

Schulzegahmen et al., 1993
Schulzegahmen, U., Rini, J. M. & Wilson, I. A. (1993).
Detailed analysis of the free and bound conformations of an antibody -- X-ray structures of Fab 17/9 and 3 different Fab-peptide complexes. J. Mol. Biol. 234, 1098-1118.

Siddiqui & Barton, 1995
Siddiqui, A. S. & Barton, G. J. (1995).
Continuous and discontinuous domains -- an algorithm for the automatic-generation of reliable protein domain definitions. Prot. Sci. 4, 872-884.

Sippl, 1990
Sippl, M. J. (1990).
Calculation of conformational ensembles from potentials of mean force -- an approach to the knowledge-based prediction of local structures in globular-proteins. J. Mol. Biol. 213, 859-883.

Smith & Waterman, 1981
Smith, T. F. & Waterman, M. S. (1981).
Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.

Sonnhammer & Kahn, 1994
Sonnhammer, E. L. L. & Kahn, D. (1994).
Modular arrangement of proteins as inferred from analysis of homology. Prot. Sci. 3, 482-492.

Stanfield et al., 1993
Stanfield, R. L., Takimotokamimura, M., Rini, J. M., Profy, A. T. & Wilson, I. A. (1993).
Major antigen-induced domain rearrangements in an antibody. Structure 1, 83-93.

Sternberg & Thornton, 1976
Sternberg, M. J. E. & Thornton, J. M. (1976).
On the conformation of proteins: the handedness of the beta-strand - alpha-helix - beta-strand unit. J. Mol. Biol. 105, 367-382.

Swindells, 1995a
Swindells, M. B. (1995a).
A procedure for detecting structural domains in proteins. Prot. Sci. 4, 103-112.

Swindells, 1995b
Swindells, M. B. (1995b).
A procedure for the automatic-determination of hydrophobic cores in protein structures. Prot. Sci. 4, 93-102.

Taylor, 1986
Taylor, W. R. (1986).
Identification of protein-sequence homology by consensus template alignment. J. Mol. Biol. 188, 233-258.

Taylor, 1997
Taylor, W. R. (1997).
Multiple sequence threading: An analysis of alignment quality and stability. J. Mol. Biol. 269, 902-943.

Taylor & Orengo, 1989
Taylor, W. R. & Orengo, C. A. (1989).
Protein-structure alignment. J. Mol. Biol. 208, 1-22.

Taylor & Thornton, 1984
Taylor, W. R. & Thornton, J. M. (1984).
Recognition of super-secondary structure in proteins. J. Mol. Biol. 173, 487-514.

Taylor et al., 1983
Taylor, W. R., Thornton, J. M. & Turnell, W. G. (1983).
An ellipsoid approximation of protein shape. J. Mol. Graph. 1, 30-38.

Thomas et al., 1996
Thomas, D. J., Casari, G. & Sander, C. (1996).
The prediction of protein contacts from multiple sequence alignments. Protein Eng. 9, 941-948.

Thomas & Dill, 1996
Thomas, P. D. & Dill, K. A. (1996).
Statistical potentials extracted from protein structures -- how accurate are they? J. Mol. Biol. 257, 457-469.

Thompson et al., 1994
Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994).
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nuc. Ac. Res. 22, 4673-4680.

Tomii & Kanehisa, 1996
Tomii, K. & Kanehisa, M. (1996).
Analysis of amino-acid indexes and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36.

Tsai & Nussinov, 1997
Tsai, C. J. & Nussinov, R. (1997).
Hydrophobic folding units derived from dissimilar monomer structures and their interactions. Prot. Sci. 6, 24-42.

Tulip et al., 1992
Tulip, W. R., Varghese, J. N., Laver, W. G., Webster, R. G. & Colman, P. M. (1992).
Refined crystal-structure of the influenza virus-N9 neuraminidase NC41 Fab complex. J. Mol. Biol. 227, 122-148.

Unger & Moult, 1993
Unger, R. & Moult, J. (1993).
Genetic algorithms for protein folding simulations. J. Mol. Biol. 231, 75-81.

Urfer & Kirschner, 1992
Urfer, R. & Kirschner, K. (1992).
The importance of surface loops for stabilizing an eightfold beta-alpha barrel protein. Prot. Sci. 1, 31-45.

Van-Heel, 1991
Van-Heel, M. (1991).
A new family of powerful multivariate statistical sequence- analysis techniques. J. Mol. Biol. 220, 877-887.

Varghese et al., 1994
Varghese, J. N., Garrett, T. P. J., Colman, P. M., Chen, L., Hoj, P. B. & Fincher, G. B. (1994).
3-dimensional structures of 2 plant beta-glucan endohydrolases with distinct substrate specificities. Proc. Natl. Acad. Sci. USA 91, 2785-2789.

Wallace et al., 1996
Wallace, A. C., Laskowski, R. A. & Thornton, J. M. (1996).
Derivation of 3D coordinate templates for searching structural databases -- application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Prot. Sci. 5, 1001-1013.

Wang, 1994
Wang, Z. X. (1994).
Assessing the accuracy of protein secondary structure. Nature: Struct. Biol. 1, 145-146.

Ward, 1963
Ward, J. H. (1963).
Hierachical grouping to optimize an objective function. J. Am. Statist. Assoc. 58, 236-244.

Webster et al., 1994
Webster, D. M., Henry, A. H. & Rees, A. R. (1994).
Antibody-antigen interactions. Curr. Opin. Struct. Biol. 4, 123-129.

Weiss & Schulz, 1992
Weiss, M. S. & Schulz, G. E. (1992).
Structure of porin refined at 1.8Å resolution. J. Mol. Biol. 227, 493-509.

Weiss & Kulikowski, 1991
Weiss, S. M. & Kulikowski, C. A., (1991).
Computer systems that learn.
Morgan-Kaufmann.

Wilson & Stanfield, 1994
Wilson, I. A. & Stanfield, R. L. (1994).
Antibody-antigen interactions -- new structures and new conformational-changes. Curr. Opin. Struct. Biol. 4, 857-867.

Wilson & Stanfield, 1993
Wilson, I. A. & Stanfield, R. L. (1993).
Antibody-antigen interactions. Curr. Opin. Struct. Biol. 3, 113-118.

Winter et al., 1994
Winter, G., Griffiths, A. D., Hawkins, R. E. & Hoogenboom, H. R. (1994).
Making antibodies by phage display technology. Annu. Rev. Immunol. 12, 433-455.

Wishart, 1969
Wishart, D. (1969).
An algorithm for hierachical classifications. Biometrics 25, 165-170.

Wong et al., 1995
Wong, Y. W., Kussie, P. H., Parhamiseren, B. & Margolies, M. N. (1995).
Modulation of antibody-affinity by an engineered amino-acid substitution. J. Immunol. 154, 3351-3358.

Woody, 1995
Woody, R. W. (1995).
Circular-dichroism. Meth. Enzymol. 246, 34-71.

Wu et al., 1992
Wu, C., Whitson, G., McLarty, J., Ermongkoncha, A. & Chang, T. C. (1992).
Protein classification artificial neural system. Prot. Sci. 1, 667-677.

Wu & Kabat, 1970
Wu, T. T. & Kabat, E. A. (1970).
An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J. Exp. Med. 132, 211-250.

Yang et al., 1996
Yang, A. S., Hitz, B. & Honig, B. (1996).
Free-energy determinants of secondary structure formation (3) beta-turns and their role in protein-folding. J. Mol. Biol. 259, 873-882.

Yi & Lander, 1993
Yi, T. M. & Lander, E. S. (1993).
Protein secondary structure prediction using nearest-neighbor methods. J. Mol. Biol. 232, 1117-1129.

Yip et al., 1995
Yip, K. S. P., Stillman, T. J., Britton, K. L., Artymiuk, P. J., Baker, P. J., Sedelnikova, S. E., Engel, P. C., Pasquo, A., Chiaraluce, R., Consalvi, V., Scandurra, R. & Rice, D. W. (1995).
The structure of Pyrococcus furiosus glutamate-dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. Structure 3, 1147-1158.

Zehfus, 1995
Zehfus, M. H. (1995).
Automatic recognition of hydrophobic clusters and their correlation with protein-folding units. Prot. Sci. 4, 1188-1202.

Zhang & Chou, 1992
Zhang, C. T. & Chou, K. C. (1992).
An optimization approach to predicting protein structural class from amino-acid-composition. Prot. Sci. 1, 401-408.

Zhou et al., 1992
Zhou, G. F., Xu, X. H. & Zhang, C. T. (1992).
A weighting method for predicting protein structural class from amino-acid-composition. Eur. J. Neurosci. 210, 747- 749.

Zhu, 1995
Zhu, Z. Y. (1995).
A new approach to the evaluation of protein secondary structure predictions at the level of the elements of secondary structure. Protein Eng. 8, 103-108.

Zvelebil et al., 1987
Zvelebil, M. J., Barton, G. J., Taylor, W. R. & Sternberg, M. J. E. (1987).
Prediction of protein secondary structure and active-sites using the alignment of homologous sequences. J. Mol. Biol. 195, 957-961.



Copyright Bob MacCallum - DISCLAIMER: this was written in 1997 and may contain out-of-date information.