Automated discovery of structural signatures of protein fold and function

Journal of Molecular Biology

Volumn 306, Issue 3, 2001, Pages 591-605

  Turcotte, Marcel ^a   Muggleton, Stephen H ^b   Sternberg, Michael J E ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Folding; Knowledge discovery; Protein function; Protein structure

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; COMPUTER PROGRAM; DATA BASE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; VALIDATION PROCESS;

EID: 0035936692     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.4414     Document Type: Article

References (56)

1. Structural genomics: Beyond the human genome project
2. The protein data bank
3. Inductive logic programming: Theory and methods
4. SCOP: A structural classification of proteins database
5. Assigning genomic sequences to CATH
6. Touring protein fold space with DALI/FSSP
7. The classification and origins of protein folding patterns
8. Dictionary of recurrent domains in protein structures
9. Correlation of observed fold frequency with the occurrence of local structural motifs
10. Theoretical studies of protein folding thermodynamics and kinetics
11. Nucleation mechanism in protein folding
12. The fundamentals of protein folding: Bringing together theory and experiment
13. Three-dimensional structure analysis of prosite patterns
14. The Prosite database, its status in 1999
15. Prints-S: The database formerly known as Prints
16. Automatic generation of primary sequence patterns from sets of related protein sequences
17. Identification of sequence motifs from a set of proteins with related function
18. Dictionary building via unsupervised hierarchical motif disacovery in the sequence space of natural proteins
19. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
20. Efficient discovery of conserved patterns using a pattern graph
21. A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures
22. Detection of protein three-dimensional side-chain patterns - New examples of convergent evolution
23. Discovery of local packing motifs in protein structures
24. Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
25. Determinants of a protein fold. Unique features of the globin amino acid sequences
26. Prediction of the occurence of the ADP-binding β-α-β-fold in proteins, using and amino acid sequence fingerprint
27. Distant homology recognition using structural classification of proteins
28. Protein secondary structure prediction using logic-based machine learning
29. Drug design by machine learning: The use of inductive logic programming to model the structure-activity relationships of trimethoprim analogues binding to dihydrofolate reductase
30. Quantitative structure-activity relationships by neural networks and inductive logic programming. I. The inhibition of dihydrofolate reductase by pyrimidines
31. On the use of machine learning to identify topological rules in the packing of beta-strands
32. Structure-activity relationships derived by machine learning: The use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming
33. DNA recognition by proteins with the helix-turn-helix motif
34. Rocognition of a DNA operator by the repressor 434: A view at high resolution
35. R1 complex at 2.5 Å resolution
36. Principles of sequence-dependent flexure of DNA
37. Crystal structure of trp repressor/operator complex at atomic resolution
38. Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules
39. Structural comparisons among the short-chain helical cytokines
40. Two distinct functional sites of human interleukin 4 are identified by variants impaired in either receptor binding or receptor activation
41. Supersites within superfolds. Binding site similarity in the absence of homology
42. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins
43. Editorial
44. Enhanced genome annotation using structural profiles in the program 3D-PSSM
45. Promotif - A program to identify and analyze structural motifs in proteins
46. Protein fold recognition
47. The effect of relational background knowledge on learning of protein three-dimensional fold signatures
48. CProgo14.4: Theory and use
49. Inverser entailment and progol
50. Improved tools for biological sequence analysis
51. A novel two-over-two α-helical sandwich fold is characteristic of the truncated hemoglobin family
52. The hydrophobic moment detects periodicity in protein hydrophobicity
53. Molscript: A program to produce both detailed and schematic plots of protein structures