Division of Molecular Biosciences
Department of Life Sciences
Faculty of Natural Sciences

Publications

From ISI Web of Knowledge
H-index = 64, Sum of times cited = 11,247

Contents

Recent Publications 2008 - 2004

Dobbins, S. E., Lesk, V. I. & Sternberg, M. J. E. (2008). Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci U S A 105, 10390-5.

Bennett-Lovsey, R., Herbert, A., Sternberg, M.J.E. & Kelley, L.A. (2008) Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 70,611-624.

Wass, M. N. & Sternberg, M. J. (2008). ConFunc--functional annotation in the twilight zone. Bioinformatics 24, 798-806.

Tsunoyama, K., Amini, A., Sternberg, M. J. & Muggleton, S. H. (2008). Scaffold hopping in drug discovery using inductive logic programming. J Chem Inf Model 48, 949-57.

Lesk, V. I. & Sternberg, M. J. (2008). 3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics 24, 1137-44.

Bennett-Lovsey, R. M., Herbert, A. D., Sternberg, M. J. E. & Kelley, L. A. (2008). Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 70, 611-624.

Bang, J. W., Crockford, D. J., Holmes, E., Pazos, F., Sternberg, M. J. E, Muggleton, S. H. & Nicholson, J. K. (2008). Integrative top-down system metabolic modeling in experimental disease states via data-driven Bayesian methods. J Proteome Res 7, 497-503.

Cannon, E.O., Amini, A., Bender, A., Sternberg, M. J., Muggleton, S. H., Glen, R. C., Mitchell, J. B (2007) Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds. J Comput Aided Mol Des, 21 269-80.

Amini, A., Muggleton, S. H. Lodhi, H. & Sternberg, M. J.E. (2007). A Novel Logic-Based Approach for Quantitative Toxicology Prediction. J Chem Inf Model, 2007.47, 998-1006.

Gherardini, P.R. Mark N Wass, M.N., Helmer-Citterich, H. & Sternberg, M.J.E. (2007) Convergent evolution of enzyme active sites is not a rare phenomenon. J. Mol.Biol. 372, 817-845.

Cootes, A.P., Muggelton, S.H. & Sternberg, M.J.E. (2007). The identification of similarities between biological networks: Application to the Metabolome and the Interactome. J. Mol. Biol. 369, 1126-1139.

Amini, A., Shrimpton, P. J., Muggelton, S. H. & Sternberg, M. J. E. (2007). A general approach for developing system-specfic scoring functions to score protein-liganddocked complexes using support vector inductive logic programming. Proteins 2007, 69, 823 - 831,

Tamaddoni-Nezhad, A., Chaeleil, R. A. G., Kakas, A., Sternberg, M. J. E., Nicholson, J. & Muggelton, S. H. (2007). Modeling the effects of toxins in metabolic networks. IEEE Engineering in Medicine and Biology 26, 37-46.

Jefferys, B. R., Kelley, L. A., Sergot, M. J., Fox, J. & Sternberg, M. J. E. (2006). Capturing expert knowledge with argumentation: a case study in bioinformatics. Bioinformatics 22, 924-933.

Paszkiewicz, K. H., Sternberg, M. J. E. & Lappe, M. (2006). Prediction of viable circular permutants using a graph theoretic approach. Bioinformatics 22 1353-1358.

Madhusudan, S., Smart, F., Shrimpton, P., Parsons, J. L., Gardiner, L., Houlbrook, S., Talbot, D. C., Hammonds, T., Freemont, P. A., Sternberg, M. J., Dianov, G. L. & Hickson, I. D. (2005). Isolation of a small molecule inhibitor of DNA base excision repair. Nucleic Acids Res 33, 4711-24.

Smith, G. R., Sternberg, M. J. E. & Bates, P. A. (2005) The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein-Protein Complexes with an Application to Protein-Protein Docking. J. Mol. Biol. 347, 1077-1101.

Carter, P., Lesk, V. I., Islam, S. A. & Sternberg, M. J. E. (2005) Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI. Proteins 60, 281-288.

Fernandez-Fuentes, N., Querol, E., Aviles, F. X., Sternberg, M. J. & Oliva, B. (2005) Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops. Proteins. 60, 746-757.

Pazos, F., Ranea, J. A. G., Juan, D. & Sternberg, M. J. E. (2005). Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome. J.Mol.Biol. 352, 1002-1015.

Espandaler, J., Fernandez-Fuentes, N., Hermoso, A., Querol, E., Aviles, F. X., Sternberg, M. J. E. & Oliva, B. (2004). ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acid Res. 32, D185-D188.

Fleming, K., Muller, A., MacCallum, R. M. & Sternberg, M. J. E. (2004). 3D-GENOMICS: a database to compare structural and functional annotations of proteins between genomes. Nucleic Acid Res. 32, D245-250.

Aguilar, D., Aviles, F. X., Querol, E. & Sternberg, M. J. E. (2004). Analysis of phenetic trees based on metabolic capabilities across the three domains of life. J. Mol. Biol. 340, 491-512.

Mayor, L. R., Fleming, K. P., Muller, A., Balding, D. J. & Sternberg, M. J. E. (2004). Clustering of protein domains in the human genome. J. Mol. Biol. 340, 991-1004.

Pazos, F. & Sternberg, M. J. E. (2004) Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U SA 101, 14754-14759.

Key publications from earlier work

Pioneering work on the analysis of protein structure

Sternberg, M. J. E. & Thornton, J. M. (1976). On the conformation of proteins: the handedness of β-stand / ?-helix / β-strand unit J. Mol. Biol. 105, 367-382. [135 citations]

Sternberg, M. J. E. & Thornton, J.M. (1977). On the conformation of proteins: the handedness of the connection between parallel β-strands. J. Mol. Biol. 110, 269-283.[115 citations]

Sternberg, M. J. E. & Thornton, J. M. (1977). On the conformation of proteins: an analysis of β-pleated sheets. J. Mol. Biol. 110, 285-296. [64 citation]

Cohen, F. E., Sternberg, M. J. E. & Taylor, W. R. (1980). Analysis and prediction of protein β-sheet structures by a combinatorial approach. Nature, 285, 378-382. [104 citations]

Dynamic information from protein crystallography

Sternberg, M. J. E., Grace, D. E. & Phillips, D. C. (1979). Dynamic information from protein crystallography. An analysis of temperature factors from refinement of the hen egg-white lysozyme structure. J. Mol. Biol. 130, 231-252. [129 citations]

Artymiuk, P. J., Blake, C. C., Grace, D. E., Oatley, S. J., Phillips, D. C. & Sternberg, M. J. E. (1979). Crystallographic studies of the dynamic properties of lysozyme. Nature, 280, 563-568. [356 citations]

Modelling electrostatic effects in proteins

Sternberg, M. J. E., Hayes, F. R., Russell, A. J., Thomas, P. G. & Fersht, A. R. (1987). Prediction of electrostatic effects of engineering of protein charges. Nature, 330, 86-88. [184 citations]

Novel algorithms for protein sequence alignment

Barton, G. J. & Sternberg, M. J. E. (1987). A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J. Mol. Biol. 198, 327-337. [313 citations]

First relational database of protein structure

McGregor, M. J., Islam, S. A. & Sternberg, M. J. E. (1987). Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198, 295-310. [350 citations]

Recognition that poly-proline helices are widely observed in globular proteins

Adzhubei, A. A. & Sternberg, M. J. E. (1993). Left-handed poly-proline II helices commonly occur in globular proteins. J. Mol. Biol. 229, 472-493. [244 citations]

Application of machine learning to structural biology

King, R. D., Muggleton, S. H., Srinivasan, A. & Sternberg, M. J. E. (1996). Representing molecular structure activity relationships: the use of atoms and their bond connectivities to predict mutagenicity using inductive logic programming. Proc. Nat. Acad. Sci. USA, 93, 438-442. [84 citations]

Development of algorithms for accurate protein structure prediction

Russell, R. B., Saqi, M. A., Sayle, R. A., Bates, P. A. & Sternberg, M. J. E. (1997). Recognition of analogous and homologous protein folds - Analysis of sequence and structural conservation. J. Mol. Biol. 269, 423-439. [115 citations]

Kelley, L A., MacCallum, R. M. & Sternberg, M. J. E. (2000). Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299, 501-522. [928 citations]

Development of an accurate approach to model protein docking

Gabb, H. A., Jackson, R. M. & Sternberg, M. J. E. (1997). Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 272, 106-120. [264 citations]

Jackson, R. M., Gabb, H. A. & Sternberg, M. J. E. (1998). Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J. Mol. Biol. 276, 265-285.[140 citations]

Analysis and prediction of protein function

Aloy, P., Querol, E., Aviles, F. X. & Sternberg, M. J. E. (2001). Automated structure-based prediction of functional sites in proteins - Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol. 311, 395-408. [120 citations]

All Research Publications in Journals

1.Sternberg, M. J. E. & Thornton, J. M. (1976). On the conformation of proteins: the handedness of β-stand / ?-helix / β-strand unit J. Mol. Biol. 105, 367-382.

2. Sternberg, M. J. E. & Thornton, J.M. (1977). On the conformation of proteins: the handedness of the connection between parallel β-strands. J. Mol. Biol. 110, 269-283.

3.Sternberg, M. J. E. & Thornton, J. M. (1977). On the conformation of proteins: an analysis of β-pleated sheets. J. Mol. Biol. 110, 285-296.

4.Sternberg, M. J. E. & Thornton, J.M. (1977). On the conformation of proteins: hydrophobic ordering of strands in β-pleated sheets. J. Mol. Biol. 115, 1-17.

5.Sternberg, M. J. E. & Thornton, J. M. (1977). On the conformation of proteins: towards the prediction of strand arrangements in β-pleated sheets. J. Mol. Biol. 113, 401-418.

6.Phillips, D.C., Sternberg, M. J. E., Thornton, J.M. & Wilson, I.A. (1978). An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase. J. Mol. Biol. 119, 329-351.

7.Sternberg, M. J. E., Grace, D. E. & Phillips, D. C. (1979). Dynamic information from protein crystallography. An analysis of temperature factors from refinement of the hen egg-white lysozyme structure. J. Mol. Biol. 130, 231-252.

8.Artymiuk, P. J., Blake, C. C., Grace, D. E., Oatley, S. J., Phillips, D. C. & Sternberg, M. J. E. (1979). Crystallographic studies of the dynamic properties of lysozyme. Nature, 280, 563-568.

9.Cohen, F. E., Sternberg, M. J. E. & Taylor, W. R. (1980). Analysis and prediction of protein β-sheet structures by a combinatorial approach. Nature, 285, 378-382.

10.Burton, D.R., Boyd, J., Brampton, A.D., Easterbrook Smith, S.B., Emanuel, E.J., Novotny, J., Rademacher, T.W., van Schravendijk, M.R. & Sternberg, M. J. E. (1980). The Clq receptor site on immunoglobulin G. Nature, 288, 338-344.

11.Cohen, F.E., Sternberg, M. J. E., Phillips, D.C., Kuntz, I.D. & Kollman, P.A. (1980). A diffusion-collision-adhesion model for the kinetics of myoglobin refolding. Nature, 286, 632-634.

12.Cohen, F.E. & Sternberg, M. J. E. (1980). On the prediction of protein structure: The significance of the root-mean-square deviation. J. Mol. Biol. 138, 321-333.

13.Cohen, F.E. & Sternberg, M. J. E. (1980). On the use of chemically derived distance constraints in the prediction of protein structure with myoglobin as an example. J. Mol. Biol. 137, 9-22.

14.Cohen, F.E., Novotny, J., Sternberg, M. J. E., Campbell, D.G. & Williams, A.F. (1981). Analysis of structural similarities between brain Thy-1 antigen and immunoglobulin domains. Evidence for an evolutionary relationship and a hypothesis for its functional significance. Biochem.J. 195, 31-40.

15.Cohen, F.E., Sternberg, M. J. E. & Taylor, W.R. (1981). Analysis of the tertiary structure of protein β-sheet sandwiches. J. Mol. Biol. 148, 253-272.

16.Cohen, F.E., Sternberg, M. J. E. & Taylor, W.R. (1982). Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins. J. Mol. Biol. 156, 821-862.

17.Sternberg, M. J. E. & Cohen, F.E. (1982). The prediction of the secondary and tertiary structures of interferon from four homologous amino acid sequences. Int. J. Biol. Macromol. 4, 137-144.

18.Rogers, N.K. & Sternberg, M. J. E. (1984). Electrostatic Interactions in globular proteins: Different dielectric models applied to the packing of α-helices. J. Mol. Biol. 174, 527-542.

19.Sternberg, M. J. E. & Taylor, W.R. (1984). Modelling the ATP-binding site of oncogene products, the epidermal growth factor receptor and related proteins. FEBS Letts. 175, 387-392.

20.Travers, P., Blundell, T.L., Sternberg, M. J. E. & Bodmer, W.F. (1984). HLA-D homology model-building. Nature, 310, 235-238.

21.Rawlings, C.J., Taylor, W.R., Nyakairu, J., Fox, J. & Sternberg, M. J. E. (1985). Reasoning about protein topology using the logic programming language PROLOG. J. Mol. Graph. 3, 151-158.

22.Rogers, N.K., Moore, G.R. & Sternberg, M. J. E. (1985). Electrostatic interactions in globular proteins: calculation of the pH dependence of the redox potential of cytochrome c551. J. Mol. Biol. 182, 613-616.

23.Sternberg, M. J. E., Hayes, F. R., Russell, A. J., Thomas, P. G. & Fersht, A. R. (1987). Prediction of electrostatic effects of engineering of protein charges. Nature, 330, 86-88.

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

25.Bryant, S.H. & Sternberg, M. J. E. (1987). Comparison of protein structural profiles by interactive computer graphics. J.Mol.Graph. 5, 4-7.

26.Coates, A.R., Cookson, J., Barton, G.J., Zvelebil, M.J. & Sternberg, M. J. E. (1987). AIDS vaccine predictions. Nature, 326, 549-550.

27.Edwards, M.S., Sternberg, M. J. E. & Thornton, J.M. (1987). Structural and sequence patterns in the loops of β-α-&abeta; units. Prot. Eng. 1, 173-181.

28.Barton, G. J. & Sternberg, M. J. E. (1987). A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. J. Mol. Biol. 198, 327-337.

29.Sternberg, M. J. E., Barton, G.J., Zvelebil, M.J., Cookson, J. & Coates, A.R. (1987). Prediction of antigenic determinants and secondary structures of the major AIDS virus proteins. FEBS Letts. 218, 231-237.

30.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.

31.McGregor, M. J., Islam, S. A. & Sternberg, M. J. E. (1987). Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198, 295-310.

32.Akrigg, D., Bleasby, A. J., Dix, N. I. M., Findlay, J. B. C., North, A. C. T., Parry, S. D., Wootton, J. C., Bludell, T. L., Gardner, S. P., Hayes, F., Islam, S. A., Sternberg, M. J. E., Thornton, J. M. & Tickle, I. J. (1988). A protein sequence/structure database. Nature, 335, 745-746.

33.Islam, S.A. & Sternberg, M. J. E. (1989). A relational database of protein structure designed for flexible enquiries about conformation. Prot. Eng. 2, 431-442.

34.Zvelebil, M. J. J. M. & Sternberg, M. J. E. (1988). Analysis and prediction of the location of catalytic residues in enzymes. Prot. Eng. 2, 127-138.

35.Barton, G. J. & Sternberg, M. J. E. (1988). LOPAL and SCAMP: techniques for the comparison and display of protein structures. J. Mol Graph. 6, 190-196.

36.Zvelebil, M. J. J. M., Sternberg, M. J. E., Cookson, J. & Coates, A. R. M. (1988). Prediction of linear T-cell and B-cell epitopes in protein encoded by HIV-1, HIV-2 and SIV-MAC and the conservation of these sites between strains. FEBS Letts. 242, 9-21.

37.Fersht, A. R. & Sternberg, M. J. E. (1989). Can a simple function for the dielectric response model electrostatic effects in globular proteins? Prot. Eng. 2, 527-530.

38.McGregor, M. J., Flores, T. P. & Sternberg, M. J. E. (1989). Prediction of ?-turns in proteins using neural networks. Prot. Eng. 2, 521-526.

39.Sternberg, M. J. E. & Gullick, W. J. (1989). Neu receptor dimerization. Nature, 339, 587.

40.Rodaway, A. R. F., Sternberg, M. J. E. & Bentley, D. L. (1989). Similarity in membrane proteins. Nature, 342, 624.

41.Bates, P. A., McGregor, M. J., Islam, S. A., Sattentau, Q. J. & Sternberg, M. J. E. (1989). A predicted three-dimensional structure for the human immunodeficiency virus binding domains of CD4 antigen. Prot. Eng. 3, 13-21.

42.King, R. D. & Sternberg, M. J. E. (1990). A machine learning approach for the prediction of protein secondary structure. J. Mol. Biol. 216, 441-457.

43.Sternberg, M. J. E. & Islam, S. A. (1990). Local protein sequence similarity does not imply a structural relationship. Prot. Eng. 4, 125-131.

44.Sternberg, M. J. E. (1990). Inter-species sequence conservation of singly-spanning transmembrane regions. Prot. Eng. 4, 45-47.

45.Barton, G. J. & Sternberg, M. J. E. (1990). Flexible protein sequence patterns: a sensitive method to detect weak structural similarities. J. Mol. Biol. 212, 389-402.

46.Sternberg, M. J. E. & Gullick, W. J. (1990). A sequence motif in the transmembrane region of growth factor receptors with tyrosine kinase activity mediates dimerization. Prot. Eng. 3, 245-248.

47.Laughton, C. A., Neidle, S., Zvelebil, M. J. J. M. & Sternberg, M. J. E. (1990). A molecular model for the enzyme cytochrome P450-17?, a major target for the chemotherapy of prostatic cancer. Biochem. Biophys. Res. Commun. 171, 1160-1167.

48.Zvelebil, M. J. J. M., Wolf, C. R. & Sternberg, M. J. E. (1991). A predicted three-dimensional structure of human cytochrome P450: implications for substrate specificity. Prot. Eng. 4, 271-282.

49.Hirst, J. D. & Sternberg, M. J. E. (1991). Prediction of ATP-binding motifs: a comparison of a perceptron-type neural network and a consensus sequence method. Prot. Eng. 4, 615-623. [Erratum in Prot. Eng. 1993, 6, 549-54].

50.Saqi, M. A. S. & Sternberg, M. J. E. (1991). A simple method to generate non-trivial alternate alignments of protein sequences. J. Mol. Biol. 219, 727-732.

51.Islam, S. A., Wolf, C. R., Lennard, M. S. & Sternberg, M. J. E. (1991). A three-dimensional molecular template for substrates of human cytochrome P450 involved in debrisoquine 4-hydroxylation. Carcinogenesis, 12, 2211-2219.

52.Sternberg, M. J. E. (1991). Library of common protein motifs. Nature, 349, 111.

53.Sternberg, M. J. E. (1991). PROMOT: A FORTRAN program to scan protein sequences against a library of known motifs. CABIOS, 7, 257-260.

54.Pickett, S. D., Saqi, M. A. S. & Sternberg, M. J. E. (1992). Evaluation of the sequence template method for protein structure prediction - Discrimination of the (??)?8- barrel fold. J. Mol. Biol. 228, 170-187.

55.Muggleton, S., King, R. D. & Sternberg, M. J. E. (1992). Protein secondary structure prediction using logic-based machine learning. Prot. Eng. 5, 647-657. [Erratum in Prot. Eng. 1993, 6, 549].

56.Saqi, M. A. S., Bates, P. A. & Sternberg, M. J. E. (1992). Towards an automatic method of predicting protein structure by homology: an evaluation of suboptimal sequence alignments. Prot. Eng. 5, 305-311.

57.Gullick, W. J., Bottomley, A. C., Lofts, F. J., Doak, D. G., Mulvey, D., Newman, R., Crumpton, M. J., Sternberg, M. J. E. & Campbell, I. D. (1992). Three dimensional structure of the transmembrane region of the proto-oncogenic and oncogenic forms of the neu protein. EMBO J. 11, 43-48.

58.Berendt, A. R., McDowall, A., Craig, A. G., Bates, P. A., Sternberg, M. J. E., Marsh, K., Newbold, C. I. & Hogg, N. (1992). The binding site on ICAM-1 for Plasmodium falciparum infected erythrocytes overlaps but is distinct from the LFA-1 binding site. Cell, 68, 71-81.

59.Burroughs, A. K., Bulter, P., Sternberg, M. J. E. & Baum, H. (1992). Molecular mimicry in liver disease. Nature, 358, 377-378.

60.Bates, P. A., Luo, J. & Sternberg, M. J. E. (1992). A predicted three-dimensional structure for the carcinoembryonic antigen (CEA). FEBS Letts. 301, 207-214.

61.Walls, P. H. & Sternberg, M. J. E. (1992). New algorithm to model protein-protein recognition based on surface complementarity - Applications to antibody-antigen docking. J. Mol. Biol. 228, 277-297.

62.King, R. D., Muggleton, S., Lewis, R. A. & Sternberg, M. J. E. (1992). Drug design by machine learning : the use of inductive logic programming to model the structure-activity relationship of trimethoprim analogues binding to dihydrofolate reductase. Proc. Nat. Acad. Sci. USA, 89, 11322-11326.

63.Jackson, R. M. & Sternberg, M. J. E. (1993). Protein surface area defined. Nature, 366, 638.

64.Adzhubei, A. A. & Sternberg, M. J. E. (1993). Left-handed poly-proline II helices commonly occur in globular proteins. J. Mol. Biol. 229, 472-493.

65.Bax, B., Blaber, M., Ferguson, G., Sternberg, M. J. E. & Walls, P. H. (1993). Prediction of the three-dimensional structures of the nerve growth factor and epidermal growth factor binding proteins (kallikreins) and an hypothetical structure of the high molecular weight complex of epidermal growth factor with its binding protein. Protein Science, 2, 1229-1241.

66.Bates, P. A., Islam, S. A. & Sternberg, M. J. E. (1993). Structure of debrisoquinium sulfate. Acta Cryst. C49, 300-303.

67.Baum, H., Butler, P., Davies, H., Sternberg, M. J. E. & Burroughs, A. K. (1993). Autoimmune disease and molecular mimicry: an hypothesis. TIBS, 18, 140-144.

68.Pickett, S. D. & Sternberg, M. J. E. (1993). Empirical scale of side-chain conformational entropy in protein folding. J. Mol. Biol. 231, 825-839.

69.Lofts, F. J., Hurst, H. C., Sternberg, M. J. E., & Gullick, W. J. (1993). Specific short transmembrane sequences can inhibit transformation by the mutant neu growth factor receptor in vitro and in vivo. Oncogene, 8, 2813-2820.

70.Saqi, M. A. S. & Sternberg, M. J. E. (1994). Identification of sequence motifs from a set of proteins with related function. Prot. Eng. 7, 165-171.

71.Sternberg, M. J. E. & Chickos, J. S. (1994). Protein side-chain conformational entropy derived from fusion data - Comparison with other empirical scales. Prot. Eng. 7, 149-155.

72.Jackson, R. M. & Sternberg, M. J. E. (1994). Application of scaled particle theory to model the hydrophobic effect: implications for molecular association and protein stability. Prot. Eng. 7, 371-383.

73.Hirst, J. D., King, R. D. & Sternberg, M. J. E. (1994). Quantitative structure-activity relationships: neural networks and inductive logic programming compared against statistical methods I. The inhibition of dihydrofolate reductase by pyrimidines. J. Comp. Aided. Mol. Design, 8, 404-420.

74.Hirst, J. D., King, R. D. & Sternberg, M. J. E. (1994). Quantitative structure-activity relationships: neural networks and inductive logic programming compared against statistical methods II. The inhibition of dihydrofolate reductase by triazines. J. Comp. Aided. Mol. Design, 8, 421-432.

75.Harrison, P. & Sternberg, M. J. E. (1994). Analysis and classification of disulphide connectivity in proteins. The entropic effect of cross-linkage. J. Mol. Biol. 244, 448-463

76.Adzhubei, A. A. & Sternberg, M. J. E. (1994). Conservation of polyproline II helices in homologous proteins: Implications for structure prediction by model building. Protein Science, 3, 2395-2410.

77.King, R. D., Clark, D. A., Shirazi, J. & Sternberg, M. J. E. (1994). On the use of machine learning to identify topological rules in the packing of ?-strands. Prot. Eng. 7, 1295-1303.

78.Jackson, R., M. & Sternberg, M. J. E. (1995). A continuum model for protein-protein interactions: Application to the docking problem. J. Mol. Biol. 250, 258-275.

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

80.Ellis, S. W., Hathurst, G. P., Smith, G., Lightfoot, T., Wong, M. M., Simula, A. P., Ackland, M. J., Sternberg, M. J. E., Lennard, M. S. & Tucker, G. T. (1995). Evidence that aspartic acid 301 is a critical substrate contact residue in the active site of cytochrome P450 2D6. J. Biol. Chem. 270, 29055-29058.

81.King, R. D., Muggleton, S. H., Srinivasan, A. & Sternberg, M. J. E. (1996). Representing molecular structure activity relationships: the use of atoms and their bond connectivities to predict mutagenicity using inductive logic programming. Proc. Nat. Acad. Sci. USA, 93, 438-442.

82.Chickos, J. S. & Sternberg, M. J. E. (1995). A test of the applicability of small-molecular group additivity parameters in the estimation of fusion entropies of macromolecules. Thermochimica Acta 264, 13-26.

83.Srinivasan, A., Sternberg, M. J. E. & King, R. D. (1996). Theories for mutagenicity: a study of first-order and feature based induction. A.I. Journal 85, 277-299.

84.Strynadka, N. C. J., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B., Kuntz, I., Abagyan, R., Totrov, M., Janin, J., Cherfils, J., Zimmerman, F., Olson, A., Duncan, B., Rao, M., Jackson, R., Sternberg, M. J. E. & James, M. N. G. (1996). Molecular docking programs successfully determine the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nature Structural Biol. 3, 233-238.

85.Russell, R. B. & Sternberg, M. J. E. (1996). A novel binding site in catalase is suggested by structural similarity to the calycin superfamily Prot. Eng. 9, 107-111.

86.Harrison, P. M. & Sternberg, M. J. E. (1996). The disulphide beta-cross: From cystine geometry and clustering to classification of small disulphide-rich protein folds. J. Mol. Biol. 264, 603-623.

87.King, R. D. & Sternberg, M. J. E. (1996). Identification and Application of the Concepts Important for Accurate and Reliable Protein Secondary Structure Prediction. Protein Science, 5, 2298-2310.

88.Gabb, H. A., Jackson, R. M. & Sternberg, M. J. E. (1997). Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 272, 106-120.

89.Russell, R. B. & Sternberg, M. J. E. (1997). Two new examples of protein structural similarities within the structure-function twilight zone. Prot. Eng. 10, 333-338.

90.King, R. D., Saqi, M., Sayle, R. & Sternberg, M. J. E. (1997). DSC: Public Domain Protein Secondary Structure Prediction. CABIOS, 13, 473-474.

91.Lohmeyer, M., Harrison, P. M., Kannan, S., DeSantis, M., O'Reilly, N. J., Sternberg, M. J. E., Salomon, D. S. & Gullick, W. J. (1997). Chemical synthesis, structural modeling and biological activity of the epidermal growth factor-like domain of human cripto. Biochemistry, 36, 3837-3845.

92.Oliva, B., Bates, P. A., Querol, E., Aviles, F. X. & Sternberg, M. J. E. (1997). An automated classification of the structure of protein loops. J. Mol. Biol. 266, 814-830.

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

94.Gabb, H. A., Jackson, R. M. & Sternberg, M. J. E. (1997). Modelling Protein Docking using Shape Complementarity, Electrostatics and Biochemical Information. J. Mol. Biol. 272, 106-120.

95.Bates, P. A., Jackson, R. M. & Sternberg, M. J. E. (1997). Model building by comparison: A combination of expert knowledge and computer automation. Proteins, suppl 1, 59-67.

96.Jackson, R. M., Gabb, H. A. & Sternberg, M. J. E. (1998). Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J. Mol. Biol. 276, 265-285.

97.Carvin, D., Islam, S. A., Sternberg, M. J. E. & Blundell, T. L. (1998). HAD, A Databank of Heavy-Atom binding sites in protein crystals: A resource for use in multiple isomorphous replacement and anomalous scattering. Acta. Cryst. 54, 1199-1206.

98.Aloy, P., Moont, G., Gabb, H. A., Querol, E., Aviles, F. X. & Sternberg, M. J. E. (1998). Modeling repressor proteins binding to DNA. Proteins, 33, 535-549.

99.Dokurno, P., Bates, P. A., Band, H. A., Stewart, L. M. D., Taylor-Papadimitriou, J., Snary, D., Sternberg, M. J. E. & Freemont, P. S. (1998). Crystal structure at 1.95Ċ resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable recognition. J. Mol. Biol. 284, 713-728.

100.Bates, P. A., Dokurno, P., Freemont, P. & Sternberg, M. J. E. (1998). Conformational analysis of the first observed non-proline cis-peptide occurring within the complementary determining region (CDR) of an antibody. J. Mol. Biol. 284, 549-555.

101.Jackson, R. M., Gabb, H. A. & Sternberg, M. J. E. (1998). Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J. Mol. Biol. 276, 265-285.

102.Oliva, B., Bates, P. A., Querol, E., Aviles, F. X. & Sternberg, M. J. E. (1998). Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction. J. Mol. Biol. 279, 1192-1210.

103.Russell, R. B., Saqi, M. A. S., Bates, P. A., Sayle, R. A. & Sternberg, M. J. E. (1998). Recognition of analogous and homologous folds -Assessment of prediction success and associated alignment accuracy using empirical matrices. Prot. Eng. 11, 1-9.

104.Russell, R. B., Sasieni, P. D. & Sternberg, M. J. E. (1998). Supersites within superfolds - binding site similarity in the absence of homology. J. Mol. Biol. 282, 903-918.

105.Saqi, M. A. S., Russell, R. B. & Sternberg, M. J. E. (1998). Misleading local sequence alignments: implications for comparative protein modelling. Prot. Eng. 11, 627-630.

106.Zhang, X., Morera, S., Bates, P. A., Whitehead, P. C., Coffer, A. I., Hainbucher, K., Nash, R. A., Sternberg, M. J. E., Lindahl, T. & Freemont, P. S. (1998). Structure of an XRCC1 BRCT domain: a new protein-protein interaction module. EMBO J. 17, 6404-6411.

107.Betts,M. J. & Sternberg, M. J. E. (1999). An analysis of conformational changes on protein-protein association: implications for predictive docking. Prot. Eng. 12, 271-283.

108.Moont, G., Gabb, H. A. & Sternberg, M. J. E. (1999). Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 35, 364-373.

109.Bates, P. A. & Sternberg, M. J. E. (1999). Model building by comparison at CASP3: Using expert knowledge and computer automation. Proteins, Suppl. 3, 47-54.

110.Müller, A., MacCallum, R. M. & Sternberg, M. J. E. (1999). Benchmarking PSI-BLAST in genome annotation. J. Mol. Biol. 293, 1257-1271.

111.Kelley, L A., MacCallum, R. M. & Sternberg, M. J. E. (2000). Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299, 501-522.

112.Fischer, D., Bryson, K., Elofsson, A., Godzik, A., Jones, D., Karplus, K., Kelley, L. A., MacCallum, R. M., Pawlowski, K., Rost, B., Rychlewski, L. & Sternberg, M. J. E. (1999). CAFASP-1: Critical Assessment of Fully Automated Structure Prediction. Proteins Suppl. 3, 209-217.

113.MacCallum, R. M., Kelley, L. A. & Sternberg, M. J. E. (2000). SAWTED: Structure assignment with text description - enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons. Bioinformatics 16, 125-129.

114.Saqi, M. A. & Sternberg, M. J. E. (2001). A structural census of metabolic networks for E. coli. J. Mol. Biol. 313, 1195-206.

115.Turcotte, M., Muggleton, S. H. & Sternberg, M. J. E. (2001). The effect of relational backgroundknowledge on learning rules of protein three-dimensional fold signatures. Machine Learning 1,2, 81-96.

116.Turcotte, M., Muggleton, S. H. & Sternberg, M. J. E. (2001). Automated discovery of structural signatures of protein fold and function. J. Mol. Biol. 306, 591-605.

117.Aloy, P., Querol, E., Aviles, F. X. & Sternberg, M. J. E. (2001). Automated structure-based prediction of functional sites in proteins - Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol. 311, 395-408.

118.Bates, P. A., Kelley, L. A., MacCallum, R.M. & Sternberg, M. J. E. (2001). Enhancement of protein modelling by human intervention in applying the automatic prgrams 3D-JIGSAW and 3D-PSSM. Proteins CASP Supplement 5, 39-46

119.Shiels, C., Islam, S. A., Vatcheva, R., Sasieni, P., Sternberg, M. J. E., Freemont, P. S. & Sheer, D. (2001). PML bodies associate specifically with the MHC gene cluster in interphase nuclei. J Cell Sci 114, 3705-16.

120.Jennings, A. J., Edge, C. M. & Sternberg, M. J. E. (2001). An approach to improving multiple alignments of protein sequences using predicted secondary structure. Prot. Eng. 14, 227-31.

121.Vajda, S., Vakser, I. A., Sternberg, M. J. E. & Janin, J. (2002). Modeling of protein interactions in genomes. Proteins 47, 444-6.

122.Alves, R., Chaleil, R. A. & Sternberg, M. J. E. (2002). Evolution of enzymes in metabolism: a network perspective. J. Mol. Biol. 320, 751-770. [Erratum J. Mol. Biol. 2002, 22, 387].

123.Smith, G. R. & Sternberg, M. J. E. (2003). Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial. Proteins (CAPRI Supplement) 52, 74-9.

124.Cootes, A. P., Muggleton, S. H. & Sternberg, M. J. E. (2003). The automatic discovery of structural principles describing protein fold space. J. Mol. Biol. 330, 839-850.

125.Smith, G. R. & Sternberg, M. J. E. (2003). Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial. Proteins 52, 74-9.

126.Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J.E., Vajda, S., Vakser, I. & Wodak, S. J. (2003). CAPRI: A Critical Assessment of PRedicted Interactions. Proteins 52, 2-9.

127.Espandaler, J., Fernandez-Fuentes, N., Hermoso, A., Querol, E., Aviles, F. X., Sternberg, M. J. E. & Oliva, B. (2004). ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acid Res. 32, D185-D188.

128.Fleming, K., Muller, A., MacCallum, R. M. & Sternberg, M. J. E. (2004). 3D-GENOMICS: a database to compare structural and functional annotations of proteins between genomes. Nucleic Acid Res. 32, D245-250.

129.Aguilar, D., Aviles, F. X., Querol, E. & Sternberg, M. J. E. (2004). Analysis of phenetic trees based on metabolic capabilities across the three domains of life. J. Mol. Biol. 340, 491-512.

130.Mayor, L. R., Fleming, K. P., Muller, A., Balding, D. J. & Sternberg, M. J. E. (2004). Clustering of protein domains in the human genome. J. Mol. Biol. 340, 991-1004.

131.Pazos, F. & Sternberg, M. J. E. (2004) Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U SA 101, 14754-14759.

132.Madhusudan, S., Smart, F., Shrimpton, P., Parsons, J. L., Gardiner, L., Houlbrook, S., Talbot, D. C., Hammonds, T., Freemont, P. A., Sternberg, M. J., Dianov, G. L. & Hickson, I. D. (2005). Isolation of a small molecule inhibitor of DNA base excision repair. Nucleic Acids Res 33, 4711-24.

133.Smith, G. R., Sternberg, M. J. E. & Bates, P. A. (2005) The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein-Protein Complexes with an Application to Protein-Protein Docking. J. Mol. Biol. 347, 1077-1101.

134.Carter, P., Lesk, V. I., Islam, S. A. & Sternberg, M. J. E. (2005) Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI. Proteins 60, 281-288.

135.Fernandez-Fuentes, N., Querol, E., Aviles, F. X., Sternberg, M. J. & Oliva, B. (2005) Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops. Proteins. 60, 746-757.

136.Pazos, F., Ranea, J. A. G., Juan, D. & Sternberg, M. J. E. (2005). Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome. J.Mol.Biol. 352, 1002-1015.

137.Jefferys, B. R., Kelley, L. A., Sergot, M. J., Fox, J. & Sternberg, M. J. E. (2006). Capturing expert knowledge with argumentation: a case study in bioinformatics. Bioinformatics 22, 924-933.

138.Paszkiewicz, K. H., Sternberg, M. J. E. & Lappe, M. (2006). Prediction of viable circular permutants using a graph theoretic approach. Bioinformatics 22 1353-1358.

139.Cannon, E.O., Amini, A., Bender, A., Sternberg, M. J., Muggleton, S. H., Glen, R. C., Mitchell, J. B (2007) Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds. J Comput Aided Mol Des, 21 269-80.

140.Amini, A., Muggleton, S. H. Lodhi, H. & Sternberg, M. J.E. (2007). A Novel Logic-Based Approach for Quantitative Toxicology Prediction. J Chem Inf Model, 2007.47, 998-1006.

141.Gherardini, P.R. Mark N Wass, M.N., Helmer-Citterich, H. & Sternberg, M.J.E. (2007) Convergent evolution of enzyme active sites is not a rare phenomenon. J. Mol.Biol. 372, 817-845.

142.Cootes, A.P., Muggelton, S.H. & Sternberg, M.J.E. (2007). The identification of similarities between biological networks: Application to the Metabolome and the Interactome. J. Mol. Biol. 369, 1126-1139.

143.Amini, A., Shrimpton, P. J., Muggelton, S. H. & Sternberg, M. J. E. (2007). A general approach for developing system-specfic scoring functions to score protein-liganddocked complexes using support vector inductive logic programming. Proteins 2007, 69, 823 - 831,

144.Tamaddoni-Nezhad, A., Chaeleil, R. A. G., Kakas, A., Sternberg, M. J. E., Nicholson, J. & Muggelton, S. H. (2007). Modeling the effects of toxins in metabolic networks. IEEE Engineering in Medicine and Biology 26, 37-46.

145.Bennett-Lovsey, R., Herbert, A., Sternberg, M.J.E. & Kelley, L.A. (2008) Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 70,611-624.

146.Wass, M. N. & Sternberg, M. J. (2008). ConFunc--functional annotation in the twilight zone. Bioinformatics 24, 798-806.

147. Tsunoyama, K., Amini, A., Sternberg, M. J. & Muggleton, S. H. (2008). Scaffold hopping in drug discovery using inductive logic programming. J Chem Inf Model 48, 949-57.

148. Lesk, V. I. & Sternberg, M. J. (2008). 3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics 24, 1137-44.

149.Bennett-Lovsey, R. M., Herbert, A. D., Sternberg, M. J. E. & Kelley, L. A. (2008). Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 70, 611-624.

150.Bang, J. W., Crockford, D. J., Holmes, E., Pazos, F., Sternberg, M. J. E, Muggleton, S. H. & Nicholson, J. K. (2008). Integrative top-down system metabolic modeling in experimental disease states via data-driven Bayesian methods. J Proteome Res 7, 497-503.

151.Dobbins, S. E., Lesk, V. I. & Sternberg, M. J. E. (2008). Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci U S A 105, 10390-5.

Books

152.Rees, A. R. & Sternberg, M. J. E. (1984). From Cells to Atoms - An illustrated introduction to molecular biology. Blackwell Scientific, Oxford. Translated into Japanese and Russian

153.Rees, A. R., Wetzel, R. & Sternberg, M. J. E. (1992). Protein Engineering - A Practical Approach. Oxford University Press, Oxford.

154.Sternberg, M. J. E (1996) Protein Structure Prediction - A Practical Approach. Oxford University Press, Oxford.

Major reviews and conference proceedings

155.Sternberg, M. J. E. & Thornton, J.M. (1978). Prediction of protein structure from amino acid sequence. Nature, 271, 15-20.

156.Sternberg, M. J. E., Cohen, F.E., Taylor, W.R. & Feldmann, R.J. (1981). Analysis and predication of structural motifs in the glycolytic enzymes. Phil. Trans. Roy. Soc. Lond. (Biol), 293, 177-189. [Paper presented by M. J. E. S.].

157.Blundell, T.L., Sibanda, B.L., Sternberg, M. J. E. & Thornton, J.M. (1987).Knowledge-based prediction of protein structures and the design of novel molecules. Nature, 326, 347-352.

158.Sternberg, M. J. E., King, R. D., Lewis, R. A. & Muggleton, S. (1994). Application of machine learning to structural molecular biology. Phil. Trans. R. Soc. Lond. B. 344, 365-371. [Paper presented by M. J. E. S.].

159.Sternberg, M. J. E., Hegyi, H., Islam, S. A., Luo, J. & Russell, R. B. (1995). Towards an intelligent system for automatic assignment of domains in globular proteins. In "ISMB95 - Proceedings - Third International Conference on Intelligent Systems for Molecular Biology", (ed. Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. and Wodak, S.). pp. 376-383. AAAI, Menlo Park, California. [Paper presented by M. J. E. S.].

160.Sternberg, M. J. E., Aloy, P., Gabb, H. A., Jackson, R. M., Moont, G., Querol, E. & Aviles, F. X. (1998). A computational system for modelling flexible protein-protein and protein-DNA docking. In "Proceedings Sixth International Conference on Intelligent Systems for Molecular Biology", (ed. Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D. & Sensen, C.). pp. 183-192. AAAI Press, Menlo Park, California, USA. [Paper presented by M. J. E. S.].

161.Carvin, D., Islam, S. A., Sternberg, M. J. E. & Blundell, T. L. (2001). The preparation of heavy-atom derivatives of protein crystals for use in multiple isomorphous replacement. In International Tables for Crystallography (Rossmann, M. G. & Arnold, E., eds.), Vol. F, pp. 247-262. Klumer Academic, Dordrecht, Boston, London.

162.Jones, D. T., Sternberg, M. J. E. & Thornton, J. M. (2006). Bioinformatics: from molecules to systems. Phil Trans. Roy. Soc. B. 361, 389-392.

163.Fleming, K., Kelley, L. A., Islam, S. A., MacCallum, R. M., Muller, A., Pazos, F. & Sternberg, M. J. E. (2006). The proteome - structure, function and evolution. Phil Trans Roy Soc B. 361, 441-452.

Other Publications - Reviews and conference proceedings

164.Sternberg, M. J. E. & Thornton, J.M. (1978). Prediction of protein structure from amino acid sequence. Biochem. Soc. Trans. 6, 1119-1123.

165.Phillips, D.C., Rivers, P.S., Sternberg, M. J. E., Thornton, J.M. & Wilson, I.A. (1977). An analysis of the three-dimensional structure of chicken triose phosphate isomerase. Biochem. Soc. Trans. 5, 642-647.

166.Richards, F.M., Richmond, T.J., Sternberg, M. J. E. & Cohen, F.E. (1980). Formation and fluctuations of tertiary structure - the association of alpha-helices. In "Protein Folding ", (ed. Jaenicke, R.) pp.117-129. Elsevier/North Holland Biomedical Press, The Netherlands.

167.Cohen, F.E. & Sternberg, M. J. E. (1981). Theoretical aspects of protein conformation. In "Amino-acids, peptides and proteins", pp.233-240. The Royal Society of Chemistry, London.

168.Cohen, F.E. & Sternberg, M. J. E. (1981). Theoretical aspects of protein conformation. In "Amino-acids, Peptides and Proteins., pp.255-262. The Royal Society of Chemistry, London

169.Sternberg, M. J. E., Cohen, F.E. & Taylor, W.R. (1982). A combinational approach to the prediction of the tertiary fold of globular proteins. Biochem. Soc. Trans. 10, 299-301.

170.Sternberg, M. J. E. & Cohen, F.E. (1982). Interferon: a tertiary structure predicted from amino acid sequences. Phil. Trans. R. Soc. Lond. (Biol) , 299, 125-127.

171.Sternberg, M. J. E. (1983). Analysis and prediction of protein structure. In "Computing in Biological Science" (ed. Geisow, M. & Barrett, A.) pp.143-177, Elsevier Biomedical Press.

172.Blundell, T.L., Barlow, D., Thornton, J.M., Taylor, W., Tickle, I.J., Sternberg, M. J. E., Pitts, J.E., Haneef, I. & Hemmings, A.M. (1986). Three-dimensional structural aspects of the design of new protein molecules. Phil. Trans. Roy. Soc. Lond. (Biol) A317, 333-344.

173.Barlow, D.J., Blundell, T.L., Edwards, M.S., Sibanda, B.L., Sternberg, M. J. E., Taylor, W.R. & Thornton, J.M. (1986). The analysis of homologous tertiary structures and the design of novel proteins. In "Protein Engineering - applications in science, medicine and industry" (ed. Inouye, M. & Sarma, R.) pp.29-40, Academic Press.

174.Sternberg, M. J. E. (1986). Prediction of protein structure from amino acid sequence. Anticancer. Drug. Des. 1, 169-178.

175.Thornton, J.M., Barlow, B.J. & Sternberg, M. J. E. (1986). Application of computer graphics to the study of drug-receptor interactions. In "Neuropharmacology and pesticide action", pp.102-117, Horwood Ltd, Chichester.

176.Sternberg, M. J. E. (1987). Prediction of protein structure from amino acid sequence. In "Crystallography in molecular biology", (ed. Moras, D., Drenth, J., Strandberg, B., Suck, D. & Wilson, K.) pp.141-148, Plenum Press, New York.

177.Sternberg, M. J. E. (1988). Protein Modelling using Databases. pp 97-101. European Institute of Technology, Verona, Italy.

178.Blundell, T. L., Elliott, G., Gardener, S. P., Hubbard, T., Islam, S., Johnson, M., Mantafounis, D., Murray, R. P., Overington, J., Pitts, J. E., Sali, A., Sibanda, B. L., Singh, J., Sternberg, M. J. E., Sutcliffe, M. J., Thornton, J. M. & Travers, P. (1989). Protein engineering and design. Phil. Trans. Roy. Soc. Lond. B, 324, 447-460.

179.Sternberg, M. J. E. (1989). Coordinating biomolecular data. TIBS, 14, 423-424.

180.Sternberg, M. J. E., Barton, G. J., Islam, S. A., McGregor, M. J. & Zvelebil, M. J. J. M. (1989). Modelling the structure and function of proteins from their amino acid sequence using databases. In" Computer-aided Molecular Design , (ed. Richards, W.G.), pp. 157-163. IBC Technical Services Ltd, London.

181.Sternberg, M. J. E. & Islam, S. A. (1989). A relational database of protein structure. Biochemical Society Trans. 17, 845-847.

182.Sternberg, M. J. E. & Zvelebil, M. J. J. M. (1990). Prediction of protein structure from sequence. Eur. J. Cancer, 26, 1163-1166.

183.Islam, S. A., Sternberg, M. J. E. & Weaver, D. L. (1990). Bad contacts in protein structures. In "Accuracy and reliability of macromolecular crystal structures", (ed. Henrick, K., Moss, D. S. and Tickle, I. J.), pp. 53-62. Science and Engineering Research Council, Daresbury Laboratory, Warrington.

184.McGregor, M. J., Bates, P. A., Islam, S. A., Sternberg, M. J. E. & Sattentau, Q. J. (1990). A predicted three-dimensional structure of CD4 and the location of the HIV gp120 binding region. In "Protein Engineering - Protein Design in Basic Research, Medicine, and Industry", (ed. M.Ikehara, T.Oshima and K.Titani,) pp. 83-85. Japan Scientific Societies Press, Tokyo.

185.Sattentau, Q. J., Truneh, A., Arthos, J., Healey, D., Sternberg, M. J. E., Beverley, P. C. L. & Sweet, R. (1990). Idiotype vaccines for HIV based on CD4 antibodies. In "Idiotype Networks in Biology and Medicine", (ed. Osterhause, A. D. M. E. and UytdeHaag, F. G. C. M.), pp. 279-285. Elsevier, Amsterdam.

186.Sternberg, M. J. E. (1990). Deciphering the protein folding code. TIBS, 15, 360-361.

187.Sternberg, M. J. E. & Islam, S. A. (1991). Protein sequences - homologies and motifs. Trends in Biotechnology, 9, 300-302.

188.Sternberg, M. J. E. & Gullick, W. J. (1992). A sequence motif in the transmembrane region of tyrosine kinase growth factor receptors. In "Patterns in Protein Sequence and Structure", (ed. Taylor, W. R.), pp. 255-262, Springer-Verlag, Berlin.

189.Bates, P. A. & Sternberg, M. J. E. (1992). From protein sequence to structure. In "Protein Engineering - A Practical Approach", (ed. Rees, A. R., Sternberg, M. J. E. and Wetzel, R.). pp. 117-141. Oxford University Press, Oxford.

190.Sternberg, M. J. E., Lewis, R. A., King, R. D. & Muggleton, S. (1992). Modelling the structure and function of enzymes by machine learning. The Royal Society of Chemistry: Faraday Discussion, 93, 269-280.

191.Sternberg, M. J. E. (1992). Secondary structure prediction. Curr. Opin. in Struct. Biol. 2, 237-241.

192.Hirst, J. D. & Sternberg, M. J. E. (1992). Prediction of structural and functional features of proteins and nucleic acid sequences by artificial neural networks. Biochemistry, 31, 7211-7218

193.Muggleton, S., King, R. D. & Sternberg, M. J. E. (1992). Using logic for protein structure prediction. In "Proceedings of the 25th Hawaii International Conference on System Sciences", IEEE Computer Society Press, Los Alamos.

194.King, R. D., Hirst, J., D, & Sternberg, M. J. E. (1993). New approaches to QSAR : Neural networks and machine learning. Perspectives in Drug Discovery and Design, 1, 279-290.

195.King, R. D., Muggleton, S., Srinivasan, A., Feng, C., Lewis, R. A. & Sternberg, M. J. E. (1993). Drug design using inductive logic programming. In "Proceedings of the 26th Hawaii International Conference on System Sciences", pp 646-655. IEEE Computer Society Press, Los Alamos.

196.Luo, J.-c., Bates, P. A. & Sternberg, M. J. E. (1993). Knowledge-based computer modelling for the N-terminal domain of carcinoembryonic antigen (CEA). In "Peptides. Biology and Chemistry. Proceedings of the 1992 Chinese Peptide Symposium", (ed. Du, Y.-c., Tam, J. P. and Zhang, Y.-s.). pp. 115-119. ESCOM, Leiden.

197.Sternberg, M. J. E., Hirst, J. D., Lewis, R. A., King, R. D., Srinivasan, A. & Muggleton, S. (1994). Application of machine learning to protein structure prediction and drug design. In "Advances in Molecular Bioinformatics", (ed. Schulze-Kremer, S.), pp. 1-8. IOS Press, Amsterdam.

198.Sternberg, M. J. E., Lewis, R. A., King, R. D. & Muggleton, S. (1994). Machine learning and biomolecular modelling. In "Machine Intelligence, ed. 13", pp. 193-212. Oxford University Press, Oxford.

199.King, R. D., Clark, D. A., Shirazi, J. & Sternberg, M. J. E. (1994). Inductive logic programming used to discover topological constraints in protein structures. In "Second International Conference on Intelligent Systems for Molecular Biology", pp. 219-226. AAAI Press, Menlo Park.

200.Luo, J.-C., Liu, Q., Coombers, C. R., Bates, P. A. & Sternberg, M. J. E. (1994). Prediction of the three-dimensional structure of activin. In "Peptides. Biology and Chemistry. Proceedings of the 1994 Chinese Peptide Symposium", (ed. Lu, G., Tam, J. P. and Cai, M.). pp 115-119. ESCOM, Leiden.

201.King, R. D., Srinivasan, A. & Sternberg, M. J. E. (1995). Relating chemical activity to structure: an examination of ILP successes. New Gen. Computing 13, 411-433.

202.King, R. D., Sternberg, M. J. E., Srinivasan, A. & Muggleton, S. H. (1995). Knowledge discovery in a database of mutagenic chemicals. In "Proceedings of the MLnet Familiarization Workshop: Statistics, Machine Learning, and Knowledge Discovery" (ed. Kodratoff, Y., Nakaeizadeh, R. & Taylor, C.).

203.Russell, R.B. & Sternberg, M. J. E. (1995) How good are we? Current Biology, 5, 488-490.

204.King, R. D., Clark, D. A., Shirazi, J. & Sternberg, M. J. E. (1995). Discovery of protein structural constraints in a deductive database using inductive logic programming. In "Machine Intelligence, ed. 14", 27-1269, Clarendon Press, Oxford.

205.King, R. D., Hirst, J. D. & Sternberg, M. J. E. (1995). A comparison of artificial intellignece methods for modelling pharmaceutical QSARs. Applied Artificial Intelligence, 9, 213-233.

206.Srinivasan, A., Muggleton, S., King, R. D. & Sternberg, M. J. E. (1995). Mutagenesis: ILP experiments in a non-determinate biological domain In "Proceedings of the Inductive Logic Programming 1994 Workshop".

207.Doig, A. J. & Sternberg, M. J. E. (1995). Side chain conformational entropy in protein folding. Protein Science, 4, 2247- 2251.

208.Sternberg, M. J. E. (1995) Protein Modelling. In "Oxford Textbook of Oncology" (ed. Peckham, M.), pp 468-474. Oxford University Press, Oxford.

209.Bates, P. A., Jackson, R. M. & Sternberg, M. J. E. (1996). Prediction of Protein Structure and their Docking. In "Genomes, Molecular Biology and Drug Discovery", (ed. Browne, M. J. and Thurlby, P. L.). pp. 73- 88, Academic Press, London.

210.Sternberg, M. J. E. (1996). Protein Structure Prediction - Principles and Approaches. In "Protein Structure Prediction - A Practical Approach", (ed. Sternberg, M. J. E.). pp 1-30. Oxford University Press, Oxford.

211.Brutlag, D. L. & Sternberg, M. J. E. (1996). Sequences And Topology - Challenges For Algorithms And Experts - Editorial Overview. Curr. Opin. in Struct. Biol. 6, 343-345.

212.King, R. D., Clark, D. A., Shirazi, J. & Sternberg, M. J. E. (1996). Discovery of protein structural constraints in a deductive data base using inductive logic programming. In Machine Intelligence (Furukawa, K., Michie, D. & Muggleton, S., eds.), Vol. 14, pp. 271-298. Oxford University Press, Oxford.

213.Srinivasan, A., King, R. D., Muggleton, S. H. & Sternberg, M. J. E. (1997). Carcinogenesis predictions using ILP. In "Proceedings of 7th Inductive Logic Programming Workshop. Lecture Notes in Artificial Intelligence 1297", pp. 273-287. Springer Verlag, Berlin.

214.Srinivasan, A., King, R. D., Muggleton, S. H. & Sternberg, M. J. E. (1997). The predictive toxicology evaluation challenge. In "Fifteenth International Joint Conference on Artificial Intelligence", pp. 4-9. Morgan Kaufmann, San Francisco.

215.Muggleton, S., Srinivasan, A., King, R. D. & Sternberg, M. J. E. (1998). Biochemical knowledge discovery using inductive logic programming. Discovery Science, 98, pp. 326-341.

216.King, R. D., Sternberg, M. J. E., Muggleton, S. H. & Srinivasan, A. (1998). Recent developments in applying machine learning to drug design. In "Structure-Based Drug Design: Experimental and Computational Approaches "(ed. Codding, P. W.). Kluwer Academic Publishers, Dordrecht.

217.Turcotte, M., Muggleton, S. H. & Sternberg, M. J. E. (1998). Application of Inductive Logic Programming to Discover Rules Governing the Three-Dimensional Topology of Protein Structure. In "Proc. 8th International Conference on Inductive Logic Programming (ILP-98)", (ed. Page, C. D.). pp. 53-64. LNAI 1446, Spinger Verlag, Berlin.

218.Sternberg, M. J. E., Gabb, H. A. & Jackson, R. M. (1998). Predictive docking of protein-protein and protein-DNA complexes. Curr. Opin in Struct. Biol. 8, 250-256.

219.Kelley, L. A., MacCallum, R. M. & Sternberg, M. J. E. (1999). Recognition of remote protein homologies using three-dimensional information to generate a point specific scoring matrix in the program 3D-PSSM. In "RECOM99 - Proceedings of the third annual conference on computational biology", (ed. Istrail, S., Pevzner, P. and Waterman, M.). pp. 218-225. Association for Computing Machinery, New York.

220.Turcotte, M., Muggleton, S. H. & Sternberg, M. J. E. (1999). Learning rules which relate local structure to specific protein taxonomic classes. In "Machine Intelligence 16", (DeReat, L., ed.). Springer-Verlag, Berlin.

221.Sternberg, M. J. E., Bates, P. A., Kelley, L. A. & MacCallum, R. M. (1999). Progress in protein structure prediction: assessment of CASP3. Curr. Opin. in Struct. Biol. 9, 368-373.

222.Sternberg, M. J. E., Gabb, H. A., Jackson, R. M. & Moont, G. (2000). Protein-protein docking - generation and filtering of complexes. In Protein Structure Prediction: Methods and Protocols ", (ed. Webster, D.). The Humana Press, Totowa.

223.Turcotte, M., Muggelton, S. H. & Sternberg, M. J. E. (2000). Use of inductive logic programming to learn principles of protein structure. Electronic Transactions in Artificial Intelligence 4, 119-124.

224.Turcotte, M., Muggleton, S. H. & Sternberg, M. J. E. (2001). Generating protein three-dimensional fold signatures using inductive logic programming. Computers in Chemistry 26, 57-64.

225.Sternberg, M. J. E. & Moont, G. (2002). Modelling protein-protein and protein-DNA docking. In "Bioinformatics- From Genomes to Drugs" (Lengauer, T., ed.), pp. 361-404. Wiley-VCH, Weinheim.

226.Smith, G. R. & Sternberg, M. J. E. (2002). Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12, 28-35.

227.Stapley, B. J., Kelley, L. A. & Sternberg, M. J. E. (2002). Predicting the sub-cellular location of proteins from text using support vector machines. Pac Symp Biocomput, 374-85.

228.Sternberg, M. J. E. & Muggleton, S. H. (2003). Structure activity relationships (SAR) and pharmacophore discovery using inductive logic programming (ILP). QSAR and Combinatorial Science 22, 527-53

229.Muggleton, S. H., Lodhi, H., Amini, A. & Sternberg, M. J. E. (2005). Proceedings of the 8th International Conference on Discovery Science, LNAI 3735.

230.Muggelton, S. H., Lodhi, H., Amini, A. & Sternberg, M. J. E. (2005). Proceedings of the Fourth International Conference on Machine Learning and Applications, ICMLA'05, IEEE Computer Society.

231.Tamaddoni-Nezhad, A., Chaeleil, R. A. G., Kakas, A., Sternberg, M. J. E., Nicholson, J. & Muggelton, S. H. (2007). Modeling the effects of toxins in metabolic networks. IEEE Engineering in Medicine and Biology 26, 37-46.

Last update 9 Jan 2009