Cyrus Chothia: Chronological List of Publications
1. Chothia, C. & Pauling, P. Conformations of acetylcholine. Nature 219, 1156-1157
(1968).
2. Chothia, C. & Pauling, P. The structure of the potent muscarinic agonist L-(+)-acetyl-methylcholine iodide. J. Chem. Soc. Chem. Commun. 626-627 (1969).
3. Chothia, C. & Pauling, P. Two conformations of the cholinergic agonist acetyl-methylcholine: a new conformation for cholinergic molecules. J. Chem. Soc.
Chem. Commun. 746-747 (1969).
4. Chothia, C. & Pauling, P. Conformation of cholinergic molecules relevant to
acetylcholinesterase. Nature 223, 919-921 (1969).
5. Chothia, C. & Pauling, P. On the conformation of hallucinogenic molecules and their
correlations. Proc. Natl. Acad. Sci. USA 63, 1063-1070 (1969).
6. Chothia, C. & Pauling, P. The conformation of cholinergic molecules at nicotinic
nerve receptors. Proc. Natl. Acad. Sci. USA 65, 477-482 (1970).
7. Chothia, C. Interaction of acetylcholine with different cholinergic nerve receptors.
Nature 225, 36-41 (1970).
8. Chothia, C., Pauling, P. & Petcher, T.J. The conformation of cholinergic agonists.
Brit. J. Pharmacol. 39, 219P (1970).
9. Chothia, C. & Pauling, P. Absolute configurations of cholinergic molecules: the
crystal structure of (+)-trans-2-acetoxy cyclopropyl trimethylammonium iodide.
Nature 226, 541-542 (1970).
10. Chothia, C. Structure activity relationships of some muscarinic agonists. Nature 227,
1355-1356 (1970).
11. Chothia C., & Pauling P. Molecular Models. Nature 229, 281 (1971)
12. Baker, R.W., Chothia, C., Pauling, P. & Petcher, T.J. Structure and activity of
muscarinic stimulants. Nature 230, 439-445 (1972).
13. Baker, R.W., Chothia, C., Pauling, P. & Weber, H.P. Molecular structure of LSD.
Science 178, 614-615 (1972).
1
14. Baker, R.W., Chothia, C., Pauling, P. & Weber, H.P.
Molecular structures of
hallucinogenic substances: lysergic acid diethylamide, psilocybin and 2,4,5trimethoxyamphetamine. Mol. Pharm.. 9, 23-32 (1973).
15. Baker, R.W., Chothia, C. & Pauling, P. Conformation of acetylcholine at muscarinic
nerve receptors: crystal and molecular structure of 2-trimethylammoniummethyl-5-methyl furan iodide. J. Mol. Biol. 105, 517-526 (1976).
16. Chothia, C. & Pauling, P. The crystal and molecular structure of DL-lactoylcholine
iodide. Acta Cryst. B33, 1851-1854 (1977).
17. Chothia, C. & Pauling, P. The crystal and molecular structure and absolute
configuration of L-(+)-S-acetyl--methylcholine iodide. Acta Cryst. B34, 152155 (1978).
18. Chothia, C. & Pauling, P. The crystal and molecular structure and absolute
configuration of (+)-(1S, 2S)-trans-acetoxycyclopropyltrimethylammonium.
Acta Cryst. B34, 156-160 (1977).
19. Chothia, C. & Pauling, P. The crystal and molecular structure of 1,1-dimethyl-4phenylpiperazinium iodide. Acta Cryst. B34, 2986-2989 (1978).
20. Chothia, C. Conformation of twisted -sheets in proteins. J. Mol. Biol. 75, 295-302
(1973).
21. Chothia, C. Hydrophobic bonding and accessible surface area in proteins. Nature
248, 338-339 (1974).
22. Chothia, C. X-ray studies of proteins and amino acids. in Amino-acids, Peptides and
Proteins. vol. 6, pp163-205. Chemical Society. London (1974).
23. Sweet, R.M., Wright, H.T., Janin, J., Chothia, C. & Blow, D.M. Crystal structure of
the complex of porcine trypsin with soybean trypsin inhibitor (Kunitz) at 2.6 Å
resolution. Biochemistry 13, 4212-4228 (1974).
24. Chothia, C. Structural invariants in protein folding. Nature 254, 304-308 (1975).
25. Chothia, C. Acetylcholinesterase: the structure of crystals of a globular form from
electric eel. J. Mol. Biol. 97, 55-60 (1975).
26. Chothia, C. & Janin, J. Principles of protein-protein recognition. Nature 256, 705708 (1975).
2
27. Janin, J. & Chothia, C. Stability and specificity of protein-protein interactions: the
case of the trypsin-trypsin inhibitor complexes.
(1976).
J. Mol. Biol. 100, 197-211
28. Levitt, M. & Chothia, C. Structural patterns in globular proteins. Nature 261, 552558 (1976).
29. Chothia, C. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol.
105, 1-14 (1976).
30. Chothia, C., Wodak, S. & Janin, J. Role of subunit interfaces in the allosteric
mechanism of haemoglobin. Proc. Natl. Acad. Sci. USA 73, 3793-3797 (1976).
31. Chothia, C., Levitt, M. & Richardson, D. Structure of proteins: packing of -helices
and pleated sheets. Proc. Natl. Acad. Sci. USA 74, 4130-4134 (1977).
32. Janin, J. & Chothia, C. Role of hydrophobicity in the binding of coenzymes.
Biochemistry 17, 2943-2948 (1978).
33. Chothia, C. & Janin, J. Geometrical principles that determine the three dimensional
structure of proteins. in 12th FEBS meeting: Proteins: structure, function and
industrial applications. Vol. 52, pp. 117-126. Pergamon Press, Oxford (1978).
34. Janin, J. & Chothia, C. Structural aspects of protein interactions: accessible surface
area and the role of hydrophobicity. in 12th FEBS meeting: Proteins: structure,
function and industrial applications. Vol. 52, pp. 227-237. Pergamon Press,
Oxford (1978).
35. Baldwin, J. & Chothia, C. Haemoglobin: the structural changes related to ligand
binding and its allosteric mechanism. J. Mol. Biol. 129, 175-220 (1979).
36. Lesk, A.M. & Chothia, C. How different amino acid sequences determine similar
protein structures: the structure and evolutionary dynamics of the globins. J.
Mol. Biol. 136 225-268 (1980).
37. Chothia, C. & Lesk, A.M. Protein evolution and helix packing in the globins. in
Protein Folding. pp. 63-77. ed. R. Jaenicke, Elsevier-North Holland, Amsterdam
(1979).
38. Chothia, C. Concluding remarks. in Protein Folding. pp. 583-585 ed. R. Jaenicke,
Elsevier-North Holland, Amsterdam (1979).
39. Lesk, A.M. & Chothia, C. Solvent accessibility, protein surfaces and protein folding.
Biophys. J. 32, 35-42 (1980).
3
40. Janin, J. & Chothia, C. Packing of -helices onto -sheets and the anatomy of 
proteins. J. Mol. Biol. 143, 95-128 (1980).
41. Chothia, C., Levitt, M. & Richardson, D. Helix to helix packing in proteins. J. Mol.
Biol. 145, 215-250 (1981).
42. Chothia, C. & Janin, J. Relative orientation of close-packed -pleated sheets in
proteins. Proc. Natl. Acad. Sci. USA 78, 4146-4150 (1981).
43. Janin, J. & Chothia, C. The anatomy of  proteins. in Structural Aspects of
Recognition and Assembly in Biological Macromolecules. eds. M. Balaban, J.L.
Sussman, W. Traul and A. Yonath. Balaban ISS (1981).
44. Mauguen, Y., Hartley, R.W., Dodson, E.J., Dodson, G.G., Bricogne, G., Chothia, C.
& Jack, A.. Molecular structure of a new family of ribonucleases. Nature 297,
162-164 (1982).
45. Chothia, C. & Janin, J. Orthogonal packing of -pleated sheets in proteins.
Biochemistry 21, 3955-3965 (1982).
46. Chothia. C. & Lesk, A.M. The evolution of proteins formed by -sheets: I.
plastocyanin and azurin. J. Mol. Biol. 160, 309-323 (1982).
47. Lesk, A.M. & Chothia. C. The evolution of proteins formed by -sheets: II. the core
of the immunoglobulin domains. J. Mol. Biol. 160, 325-342 (1982).
48. Baldwin, J. & Chothia, C. Deoxy and liganded haemoglobin: the differences in
structure and their relation to cooperativity in ligand binding. in Hemoglobin and
oxygen binding. pp. 119-123 ed, Chien Ho, Elsevier-North Holland, Amsterdam
(1982).
49. Chothia, C. Coiling of -pleated sheets. J. Mol. Biol. 163, 107-117 (1983).
50. Chothia, C., Lesk, A.M., Dodson, G.G. & Hodgkin, D.M.C. Transmission of
conformational change in insulin. Nature 302, 500-505 (1983).
51. Lesk, A.M. & Chothia, C. Mechanisms of domain closure in proteins. J. Mol. Biol.
174, 175-191 (1984).
52. Dodson, G., & Chothia C, Protein Crystallography: 50 Years of Pepsin Crystals.
Nature 309, 309 (1984).
53. Chothia, C. Principles that determine the structure of proteins. Ann. Rev. Biochem.
53, 537-572 (1984).
4
reprinted in Protein and Nucleic Acid Structure and Dynamics pp. 39-74 ed J.
King. Benjamin/Cummings, Menlo Park (1985).
54. Chothia, C. & Lesk, A.M. Helix movements and the reconstruction of the haem
pocket during the evolution of the cytochrome c family. J. Mol. Biol. 182, 151158 (1985).
55. Lesk, A.M., Janin, J., Wodak, S. & Chothia, C. Haemoglobin: the surface buried
between the 11 and 22 dimers in the deoxy and oxy structures. J. Mol. Biol.
183, 267-270 (1985).
56. Chothia, C. & Lesk, A.M. Helix movements in proteins. Trends Biochem. Sci. 10,
116-118 (1985).
57. Chothia, C., Novotny, J., Bruccoleri, R. & Karplus, M. Domain associations in
immunoglobulin molecules: I. the packing of variable domains. J. Mol. Biol.
186, 651-663 (1985).
58. Janin, J. & Chothia, C. Domains in proteins: definitions, location and structural
principles. in Meth. Enzym. 115, 420-430 Academic Press, New York (1985).
59. Lesk, A.M. & Chothia, C. The response of protein structures to amino acid sequence
changes. Phil. Trans R. Soc. Lond. A 317, 345-356 (1986).
60. Chothia, C. & Lesk, A.M. The relation between the divergence of sequence and
structure in proteins. EMBO J. 5, 823-826 (1986).
61. Chothia, C., Lesk, A.M., Levitt, M., Amit, A.G., Mariuzza, R.A., Phillips, S.E.V. and
Poljak, R.J. The predicted structure of immunoglobulin D1.3 and its comparison
with the crystal structure. Science 233, 755-758 (1986).
62. Lesk, A.M., Levitt, M. & Chothia, C. Alignment of the amino acid sequences of
distantly related proteins using variable gap penalties.
(1986).
Prot. Eng. 1, 77-78
63. Chothia, C. & Lesk, A.M. The "crystalline molecule" image of proteins. Gazz. Chim.
Ital. 116, 557-560 (1986).
64. Bashford, D., Chothia, C. & Lesk, A.M. Determinants of a protein fold: unique
features of the globin amino acid sequences. J. Mol. Biol. 196, 199-216 (1987).
65. Miller, S., Janin, J. Lesk, A.M. & Chothia, C. Interior and surface of monomeric
proteins. J. Mol. Biol. 196, 641-656 (1987).
5
66. Chothia, C. & Lesk, A.M. Canonical structures for the hypervariable regions of
immunoglobulins. J. Mol. Biol. 196, 901-916 (1987).
67. Miller, S., Lesk, A.M., Janin, J. & Chothia, C. The accessible surface area and
stability of oligomeric proteins. Nature 328, 834-836 (1987).
68. Chothia, C. & Lesk, A.M. The evolution of protein structures. Cold Spring Habor
Symp. Quant. Biol. 52, 399-405 (1987).
69. Miller, S., Janin, J. & Chothia, C. Protein-protein interfaces in oligomeric proteins.
in Protein Recognition of Immobilised Ligands. ed. T. William Hutchens, UCLA
symposia on molecular and cellular biology, new series. Vol. 80, pp. 193-202.
Alan R. Liss Inc., New York (1988).
70. Chothia, C. Protein structure: the fourteenth barrel rolls out. Nature 333, 598-599
(1988).
71. Lesk, A.M. & Chothia, C. Elbow motion in the immunoglobulins involves a
molecular ball-and-socket joint. Nature 335, 188-190 (1988).
72. Janin, J., Miller, S. & Chothia, C. Surface, subunit interfaces and interior of
oligomeric proteins. J. Mol. Biol. 204, 155-164 (1988).
73. Chothia, C., Boswell, D.R. & Lesk, A.M. The outline structure of the T cell 
receptor. EMBO J. 7, 3745-3755 (1988).
74. Chothia, C. Polyhedra for helical proteins. Nature 337, 204-205 (1989).
75. Lesk, A.M., Branden, C.-I. & Chothia, C. Structural principles of  barrel proteins:
the packing at the interior of the sheet. Proteins 5, 139-148 (1989).
76. Creighton, T.E. & Chothia, C. Selecting buried residues. Nature 339, 14-15 (1989).
77. Chothia, C., Lesk, A.M., Tramontano, A., Levitt, M., Smith-Gill, S.J., Air, G.,
Sheriff, S., Padlan, E.A., Davies, D., Tulip, W.R., Colman, P.M. Spinelli, S.,
Alzari, P.M. & Poljak, R.J. Conformations of immunoglobulin hypervariable
regions. Nature 342, 877-883 (1989).
78. Tramontano, A., Chothia, C. & Lesk, A.M. Structural determinants of the
conformation of medium-sized loops in proteins. Proteins, 6, 382-394 (1989).
79. Chothia, C. & Finkelstein, A.V. The classification and origins of protein folding
patterns. Ann. Rev. Biochem. 59, 1007-1039 (1990).
6
80. Tramontano. A., Chothia, C. & Lesk, A.M.
Framework residue 71 is a major
determinant of the position and conformation of the second hypervariable region
in the VH domains of immunoglobulins. J. Mol. Biol. 215, 175-182 (1990).
81. Janin, J. & Chothia, C. The structure of protein-protein recognition sites. J. Biol.
Chem. 265, 16027-16030 (1990).
82. Chothia, C. Antigen Recognition. Curr. Opin. Struct .Biol. 1, 53-59 (1991).
83. Van Beeuman, J., Van Bun, S., Canters, G.W., Lommen, A. & Chothia, C. The
Structual Homology of Amicyanin from Thiobacillus versutus to Plant
Plastocyanins. J. Biol. Chem. 266, 4869-4877 (1991).
84. Chothia, C. Asymmetry in protein structures. in Ciba Found. Symp. 162: Biological
Asymmetry and Handedness. pp. 36-57 eds. G.R. Bock & J. Marsh. John Wiley.
Chichester (1991).
85. Chothia, C., & Lesk, A.M. Conformations for strand entry into parallel -sheets. In
Molecular Conformation and Biological Interactions (P. Balarum & S.
Ramaseshan, eds.) Indian Academy of Sciences, Bangalore. pp. 49-58 (1991).
86. Gerstein M. & Chothia, C. Analysis of protein loop closure: two types of hinges
produce one motion in lactate dehydrogenase.
(1991).
J. Mol. Biol. 220, 133-149
87. Stein, P. & Chothia, C. Serpin tertiary structure transformation. J. Mol. Biol. 221,
615-621 (1991).
88. Murzin, A.G., Lesk, A.M. & Chothia, C. -trefoil fold: patterns of structure and
sequence in the Kunitz inhibitors, interleukins-1and -1 and the fibroblast
growth factors. J Mol. Biol. 223, 531-543, (1992).
89. McPhalen, C.A., Vincent, M.G., Picot, D., Jansonius, J.N., Lesk, A.M. & Chothia, C.
Domain closure in mitochondrial aspartate aminotransferase. J. Mol. Biol. 227,
197-213 (1992).
90. Chothia, C. Lesk, A.M. Gherardi. E., Tomlinson, I.M. Walter, G., Marks, J.D.
Llewelyn, M.B. & Winter, G. Structural repertoire of the human VH segments.
J. Mol. Biol. 227, 799-817 (1992).
91. Chothia, C. One thousand families for the molecular biologist. Nature 357, 543-544
(1992).
7
92. Murzin A. & Chothia, C. Protein architecture: new superfamilies. Curr. Opin struct.
Biol. 2, 895-903 (1992).
93. Gerstein, M., Schulz, G. & Chothia, C. Domain closure in adenylate kinase: joints on
either side of two helices close like neighbouring fingers. J. Mol. Biol. 229, 494501 (1993).
94. Gerstein, M., Anderson, B.F., Norris, G.E., Baker, E.N., Lesk, A.M. & Chothia, C.
Domain closure in lactoferrin: two hinges produce a see-saw motion between
alternative close-packed interfaces. J. Mol. Biol. 234, 357-372 (1993).
95. Chothia, C. & Murzin, A.G. New folds for all-proteins. Structure 1, 217-222
(1993).
96. Gerstein, M., Sonnhammer, E.L.L. & Chothia, C.
evolution. J. Mol. Biol. 236, 1067-1078 (1994).
Volume changes in protein
97. Murzin, A.G., Lesk, A.M. & Chothia, C. Principles determining the structure of sheet barrels in proteins: I a theoretical analysis. J. Mol. Biol. 236, 1369-1381
(1994).
98. Murzin, A.G., Lesk, A.M. & Chothia, C. Principles determining the structure of sheet barrels in proteins: II the observed structures. J. Mol. Biol. 236, 1382-1400
(1994).
99. Harpaz Y. & Chothia, C. Many of the immunoglobulin superfamily domains that
form cell adhesion molecules and surface receptors have structures similar to
variable domains. J. Mol. Biol. 238, 528-539 (1994).
100. Gerstein, M., Lesk, A.M. & Chothia, C. Structural Mechanisms for Domain
Movements in Proteins. Biochemistry 33 6739-6749 (1994).
101. Chothia, C. & Taylor, W.R. Sequences and topology: Editorial overview. Curr.
Opin struct. Biol. 4, 381-382 (1994).
102. Harpaz, Y., Gerstein, M. & Chothia, C.
Structure 2, 641-649 (1994).
Volume changes on protein folding.
103. Chothia, C. Protein families in the metazoan genome. Development supplement:
the evolution of development, 27-33 (1994)
104. Barré, S., Greenberg, A.S., Flajnik, M.F. & Chothia, C. Structural conservation of
hypervariable regions in the evolution of the immunoglobulins. Nature
structural biology 1, 915-920 (1994).
8
105. Murzin, A.G., Brenner, S., Hubbard, T. & Chothia, C.
SCOP: the structural
classification of proteins database. J. Mol. Biol. 247, 536-540 (1995).
106. Tomlinson, I.M., Cox, J.P.L., Gherardi, E., Lesk, A.M. & Chothia, C. The structural
repertoire of the human V domains. EMBO J. 14, 4628-4638 (1995).
107. Bateman, A. & Chothia, C. Outline structures for the extracellular domains of the
fibroblast growth factor receptors. Nature structural biology 2, 1068-1074
(1995).
108. Brenner, S.E., Hubbard, T., Murzin, A. and Chothia, C. At least one third of the
proteins in Haemophilus influenzae arose from gene duplications. Nature 378,
140 (1995).
109. Brenner, S.E., Chothia, C., Hubbard, T. & Murzin, A. Understanding protein
structure: using SCOP for fold interpretation. in Meth. Enzym. 266, 635-653
Academic Press, New York (1996).
110. Gerstein, M. and Chothia, C. Packing at the Protein-Water Interface. Proc. Natl.
Acad. Sci. 93, 10167-10172 (1996)
111. Bateman, A., Eddy, S.R. and Chothia, C. Members of the Immunoglobulin
Superfamily in Bacteria. Protein Sci. 5, 1939-1941 (1996).
112. Fong, S., Hammill, S.J., Proctor, M., Freund, S.M.V., Benian, G.M., Chothia, C.,
Bycroft, M. and Clarke, J. Structure and stability of an immunoglobulin
superfamily domain from twitchin, a muscle protein of the nematode
Carnorhabdites elegans. J. Mol. Biol. 264, 624-639 (1996).
113. Bateman, A., Jouet, M., MacFarlane, J., Du, J.-S., Kenwrick, S. & Chothia, C.
Outline structure of the human L1 cell adhesion molecule and the sites where
mutations cause neurological disorders. EMBO J., 15, 6048-6057 (1996).
114. Bateman, A & Chothia, C. Fibronectin type III domains in yeast detected by a
Hidden Markov model. Curr. Biol. 6, 1544-1547 (1996).
115. Hubbard, T., Murzin, A.G., Brenner, S. & Chothia, C. SCOP: a structural
classification of proteins database. Nucleic Acids Res. 25, 236-239 (1997).
116. Chothia, C. & Gerstein, M. Protein evolution: how far can sequences diverge?
Nature 385 379-380 (1997)
117. Chothia, C. Protein-Protein and Protein-carbohydrate recognition in Molecular
aspects of host-pathogen interactions (ed. M.A. McCrae, J.R. Saunders, C.J.
9
Smyth & N.D. Stow) Society for General Microbiology Symposium 55.
Cambridge University Press, Cambridge (1997).
118. Brenner, S.E., Chothia, C. & Hubbard, T.J.P. Population statistics of protein
structures: lessons from structural classifications. Curr. Opin. Struct. Biol. 7,
369-376 (1997).
119. Chothia, C., Hubbard, T., Brenner, S., Barns, H. & Murzin A. Protein folds in the
all- and all- classes. Annu. Rev. Biophys. Biomol. Struc. 26, 597-627. (1997).
120. Chothia, C. & Jones, E.Y. Molecular structure of cell Adhesion molecules. Annu.
Rev. Biochem. 66, 823-862 (1997)
121. Sandford, R., Sgotto, B., Aparicio, S., Brenner, S., Vaudin, M., Wilson R.K.
Chissoe, S., Pepin, K., Bateman A., Chothia, C., Hughes J. & Harris P.
Comparative analysis of the polycystic kidney disease 1 (PKD1) gene reveals an
integral membrane glycoprotein with multiple evolutionary conserved domains.
Hum. Mol. Genet. 6, 1483-1489 (1997).
122. Park, J., Teichmann, S.A., Hubbard, T. & Chothia, C. Intermediate sequences
increase the detection of distant sequence homologies. J. Mol. Biol. 273, 349-354
(1997).
123. Morea, V. Tramontano, A., Rustici, M., Chothia. C., & Lesk A.M. Antibody
structure, prediction and redesign. Biophys Chem 68, 9-16 1997.
124. Al-Lazikani, B. Lesk, A. & Chothia, C. Standard conformations for the canonical
structures of immunoglobulins. J. Mol. Biol. 273, 927-948 (1997).
125. Morea, V., Tramontano, A., Rustici, M., Chothia, C. & Lesk, A. Conformations of
the third hypervariable in the VH domain of immunoglobulins. J. Mol. Biol. 275,
269-294 (1998).
126. Chothia, C., Gelfand, I. & Kister, A. Structural determinants in the sequences of
immunoglobulin variable domains. J. Mol. Biol. 278, 457-479 (1998).
127. Brenner, S.E., Chothia, C. & Hubbard T. Assessing sequence comparison methods
with reliable structurally identified distant evolutionary relationships. Proc. Natl.
Acad. Sci. USA 95, 6073-6078 (1998).
128. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T. & Chothia,
C. Sequence comparisons using multiple sequences detect three times as many
remote homologues as pairwise methods. J. Mol. Biol. 284, 1201-1210 (1998).
10
129. Hubbard, T.J.P., Ailey, B., Brenner, S.E., Murzin, A.G. & Chothia, C. SCOP,
Structural Classification of Proteins Database: applications to evaluation of the
effectiveness of sequence alignment methods and statics of protein structural
data. Acta Cryst. D54, 1147-1154 (1998).
130. Teichmann, S.A., Park, J. & Chothia C. Structural assignments to the Mycoplasma
genitalium proteins show extensive gene duplications and domain
rearrangements. Proc. Natl. Acad. Sci. USA 95, 14658-14663 (1998).
131. Hubbard, T.J.P. Ailey, B., Brenner, S.E., Murzin, A.G. & Chothia, C. SCOP: a
structural classification of proteins database. Nucleic Acids Res. 27, 254-256
(1999).
132. Bycroft, M., Bateman, A., Clarke, J., Hamill. S.J., Sandford, R., Thomas, R.L. &
Chothia, C. The structure of a PKD domain from polycystin-1: implications for
polycystic kidney disease. EMBO J. 18, 297-305 (1999)
133. Lo Conte, L., Chothia, C. & Janin, J. The atomic structure of protein-protein
recognition sites. J. Mol. Biol. 285, 2177-2198 (1999).
134. Tsai, J., Taylor, R., Chothia, C. & Gerstein M. The packing density in proteins:
standard radii and volumes. J Mol. Biol. 290, 253-266 (1999).
135. Teichmann, S.A., Chothia, C. & Gerstein M. Advances in structural genomics. Curr.
Opin. Struc. Biol. 9, 390-399 (1999).
136. Chothia, C., Lesk, A.M., Kister, A. & Gelfend, I. Why structure changes more
slowly than sequence in protein evolution. in Simplicity and Complexity in
Proteins and Nucleic Acids (ed. Frauenfelder, H., Deisenhofer, J. & Wolynes,
P.G.) Dahlem University Press, Berlin (1999).
137. Gerstein, M & Chothia, C. Proteins in Motion. Science 285, 1682-1683 (1999)
138. Lo Conte, L., Ailey, B., Hubbard, T.J.P., Brenner, S.E., Murzin, A.G. & Chothia C.
SCOP: a Structural Classification of Proteins Database. Nucleic Acids Res. 28,
257-259 (2000).
139. Hamill, S.J., Cota, E., Chothia, C. & Clarke, J. Conservation of folding and stability
within a protein family: the tyrosine corner as an evolutionary cul-de-sac. J. Mol.
Biol. 295, 641-649 (2000)
140. Al-Lazikani, B. Lesk, A. & Chothia, C. Canonical Structures for the hypervariable
regions of T cell  receptors. J. Mol. Biol. 295, 979-994 (2000).
11
141. Teichmann, S.A., Chothia, C., Church, G.M. & Park, J. Fast assignment of protein
structures to sequences using the intermediate sequence library PDB-ISL.
Bioinformatics 16, 117-124 (2000).
142. Teichmann, S.A. & Chothia, C. Immunoglobulin Superfamily Proteins in C.
elegans. J. Mol. Biol. 296, 1367-1387 (2000).
143. Park, J., Holm, L., Heger, A. & Chothia, C. RSDB; representative protein sequence
databases have high information content. Bioinformatics 16, 458-464 (2000).
144. Hill, E., Broardbent, I.D., Chothia C. & Pettitt, J. Cadherin superfamily proteins in
Caenorhabditis elegans and Drosophila melanogaster. J. Mol. Biol. 305, 10111024 (2001).
145. Teichmann, S.A., Murzin, A.G. and Chothia, C. Determination of protein function,
evolution and interactions by structural genomics. Curr. Opin. Struc. Biol. 11,
354-363. (2001).
146. Teichmann, S.A., Rison, S.C.G., Thornton J.M., Riley, M. Gough, J. & Chothia, C.
The evolution and structural anatomy of the small molecule metabolic pathways
in Escherichia coli. J. Mol. Biol. 311, 693-708 (2001).
147. Gough, J., Karplus, K., Hughey, R & Chothia, C. Assignment of homology to
genome sequences using a library of hidden Markov models that represent all
proteins of known structure. J. Mol. Biol. 313, 903-919 (2001).
148. Teichmann, S.A., Rison, S.C.G., Thornton J.M., Riley, M. Gough, J. & Chothia, C.
Small-molecue metabolism: an enzyme mosaic. Trends in Biotechnology. 19,
482-486 (2001).
149. Lo Conte, L., Brenner, S. E., Hubbard, T.J.P., Chothia, C. & Murzin, A.G. SCOP
database in 2002: refinements accomodate structural genomics. Nucleic Acids
Res. 30, 264-267 (2002).
150. Gough, J. & Chothia, C. SUPERFAMILY: HMMs representing all proteins of
known structure: SCOP sequence searches, alignments and genome assignments.
Nucleic Acids Res. 30, 268-267 (2002).
151. Bashton M. & Chothia C. The Geometry of Domain Combination in Proteins. J.
Mol. Biol. 315, 927-939 (2002).
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152. Jardine, O., Gough, J., Chothia, C. & Teichmann, S.A. Comparison of the Small
Molecule Metabolic Enzymes of Escherichia coli and Saccharomyces cerevisiae.
Genome Res 12, 916-929 (2002).
153. Hill, E.E., Morea V. & Chothia, C. Sequence conservation in families whose
members have little or no sequence similarity. J. Mol. Biol. 322, 205-233
(2002).
154.
Okazaki et al. Analysis of the mouse transcriptome based on functional
annotation of 60,770 full-length cDNAs. Nature 420, 563-573 (2002).
155. de Bono B. & Chothia C. EXEGESIS: A Procedure to Improve Gene Predictions
and its use to find Immunoglobulin Superfamily Proteins in the Human and
Mouse Genomes. Nucleic Acids Res. 31, 6096-6103 (2003)
156. Chothia, C., Gough, J., Vogel, C. & Teichmann S.A. Evolution of the Protein
repertoire. Science 300, 1701-1703 (2003).
157. Vogel, C., Teichmann S.A. and Chothia, C. The Immunoglobulin Superfamily in
Drosophila melanogaster and Caenorhabditis elegans and the Evolution of
Complexity. Development 130, 6317-6328 (2003).
158. Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J.P. Chothia, C. & Murzin,
A.G. SCOP database in 2004: refinements integrate structure and sequence
family data. Nucleic Acids Res. 32, D226-D229 (2004).
159. Madera, M., Vogel, C., Kummerfeld, S.K. Chothia C. & Gough, J. The
SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids
Res. 32 D235-D239 (2004).
160. Vogel, C., Bashton, M., Kerrison, N.D., Chothia, C. & Teichmann, S.A. Structure,
Function and Evolution of Multidomain Proteins. Curr. Opin. Struc. Biol. 14
208-216. (2004).
161. Vogel C., Teichmann S.A. & Chothia, C. Looking at the bigger picture.
Development 131, 2238-2240 (2004).
162. Gough J. & Chothia C. The Linked Conservation of Structure and Fuction in a
Family of High Diversity: the Monomeric Cupredoxins. Structure. 12, 917-925
(2004).
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163. de Bono, B. & Chothia, C. VH gene segments in the human and mouse genomes. J.
Mol. Biol. 342, 131-143 (2004).
164. Vogel C. & Chothia C. Protein family expansions and biological complexity.
PLOS Computational Biology 2, 370-382 (2006).
165. Han J.H., Kerrison N., Chothia C. & Teichmann S.A. Divergence of
interdomain geometry in two-domain proteins. Structure 14, 935-945 (2006).
166. Levy ED, Pereira-Leal JB, Chothia C & Teichmann SA. 3D complex: A
structural classification of protein complexes. PLOS Computational Biology
2, 1395-1406 (2006).
167. Wilson, D., Madera M., Vogel, C., Chothia, C. and Gough J. The
SUPERFAMILY database in 2007: families and function. Nucleic Acids Res.
35: D308-D313, (2007).
168. Bashton, M & Chothia C. The Generation of New Protein Functions by the
Combination of Domains. Structure, 15, 85-99 (2007).
169. Sasidharan, R. & Chothia C. The Selection of Acceptable Mutations. Proc. Natl.
Acad. Sci. USA 104, 10080-10085 (2007).
170. Andreeva, A., Howorth, D., Chandonia, J.-M., Brenner, E.E., Hubbard, T.J.P.
Chothia, C. & Murzin, A.G. Data Growth and its Impact on the SCOP
database: New Developments. Nucleic Acids Res. 36: D419-D425, (2008).
171. Wilson, D, Pethica, R., Zhou, Y., Talbot, C., Vogel, C., Madera, M., Chothia,
C. & Gough, J, SUPERFAMILY-sophisticated comparative genomics,
datamining, visualization and phylogeny. Nucleic Acids Res. 37, D380-D386,
(2009).
172 Chothia, C. & Gough J. Genomic and Structural Aspects of Protein Evolution.
Biochem. J. 419, 15-28 (2009).
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Journals
J. Mol. Biol. 14, 19, 24, 26, 28, 34, 35, 39, 40, 45, 46, 48, 50, 52, 53, 55, 62, 63, 64, 70,
78, 84 85, 86, 88, 89, 91, 92, 94, 95, 96, 97 (32)
Nature 1, 4, 7, 9,10, 11, 20, 23, 25, 27, 43, 49, 65, 68, 69, 72, 74, 75, 87, (19)
Proc. Natl. Acad. Sci. USA 5, 6, 29, 30, 41,
(5)
Biochemistry 22, 31, 44, 98 (4)
EMBO J. 58, 71 (2)
Science 12, 59, (2)
Structure 93, 100 (2)
J. Biol. Chem. 79, 81 (2)
Acta Cryst. 15, 16, 17, 18, (4)
J. Chem. Soc. Chem Commun. 2, 3 (2)
Ann, Rev. Biochem. 51, 77 (2)
Proteins 73, 76 (2)
Cold Spring Habor Symp Quant. Biol. 66 (1)
Prot Eng. 60 (1)
Biophys. J. 38 (1)
Mol. Pharm. 13 (1)
Phil. Trans R. Soc Lond. 57 (1)
Gazz. Chim. Ital. 61 (1)
Trends Biochem. Sci. 54 (1)
Brit. J. Pharmacol. 8 (1)
Curr. Opin. Struct Biol. 80, 90, 99 (3)
Books 21, 32, 33, 36, 37, 42, 47, 56, 67, 82, 83, (11)
15
Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T. & Chothia, C.
Sequence comparisons using multiple sequences detect three times as many
remote homologues as pairwise methods. J. Mol. Biol. 284, 1201-1210 (1998).
16