Target space for structural genomics revisited

Bioinformatics

Volumn 18, Issue 7, 2002, Pages 922-933

  Liu, Jinfeng ^a   Rost, Burkhard ^a  

^a Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN; PROTEOME;

ACCURACY; AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; CONTROLLED STUDY; EUKARYOTE; GENOMICS; HUMAN; MOLECULAR MODEL; PRIORITY JOURNAL; PROKARYOTE; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TARGETING; STRUCTURE ANALYSIS;

ARCHAEA; EUKARYOTA; PROKARYOTA;

EID: 0036322695     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.7.922     Document Type: Article

References (83)

1. Do aligned sequences share the same fold?
2. Gapped Blast and PSI-Blast: A new generation of protein database search programs
3. Domain combinations in archaeal, eubacterial and eukaryotic proteomes
4. An insight into domain combinations
5. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
6. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
7. The PROSITE database, its status in 1997
8. The protein information resource (PIR)
9. The Pfam protein families database
10. The Protein Data Bank
11. Structural genomics: An overview
12. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
13. Structural genomics: Beyond the human genome project
14. Structural proteomics of an archaeon
15. ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
16. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
17. GeneRAGE: A robust algorithm for sequence clustering and domain detection
18. EVA: Continuous automatic evaluation of protein structure prediction servers
19. EVA: Continuous automatic evaluation of protein structure prediction servers
20. Structural genomics: Bioinformatics in the driver's seat
21. Structural genomics taking shape
22. Towards a covering set of protein family profiles
23. The PROSITE database, its status in 1999
24. Protein folds and families: Sequence and structure alignments
25. Protein secondary structure prediction based on position-specific scoring matrices
26. Structure-based analysis of catalysis and substrate definition in the HIT protein family
27. Methodologies for target selection in structural genomics
28. Comparing function and structure between entire proteomes
29. Eukaryotes full of loopy proteins?
30. SCOP: A structural classification of proteins database
31. Prediction and analyis of coiled-coil structures
32. Predicting coiled coils from protein sequences
33. A combined algorithm for genome-wide prediction of protein function
34. Comparative protein structure modeling of genes and genomes
35. Accuracy of comparative modelling
36. From fold to function
37. Bench-marking PSI-BLAST in genome annotation
38. Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site
39. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
40. Structural genomics initiatives
41. CATH-A hierarchic classification of protein domain structures
42. Intermediate sequences increase the detection of distant sequence homologies
43. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
44. SMART: Identification and annotation of domains from signalling and extracellular protein sequences
45. Alignments grow, secondary structure prediction improves
46. Thousands of proteins likely to have long disordered regions
47. PHD: Predicting one-dimensional protein structure by profile based neural networks
48. Protein structures sustain evolutionary drift
49. Marrying structure and genomics
50. Twilight zone of protein sequence alignments
51. Prediction of protein secondary structure at better than 70% accuracy
52. Combining evolutionary information and neural networks to predict protein secondary structure
53. Prediction of helical transmembrane segments at 95% accuracy
54. Topology prediction for helical transmembrane proteins at 86% accuracy
55. Database of homology-derived structures and the structural meaning of sequence alignment
56. An analysis of structural instances of low complexity sequence segments
57. The HSSP database of protein structure-sequence alignments
58. Finding function through structural genomics
59. Pfam: A comprehensive database of protein domain families based on seed alignments
60. A genomic perspective on protein families
61. The COG database: A tool for genome-scale analysis of protein functions and evolution
62. Advances in structural genomics
63. Structural genomics takes off
64. Completeness in structural genomics
65. Statistics of local complexity in amino acid sequences and sequence databases
66. Analysis of compositionally biased regions in sequence databases
67. Sequence to structure alignment in comparative modeling using PrISM
68. An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance
69. An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence
70. An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments
71. ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space
72. ProtoMap: Automatic classification of protein sequences and hierarchy of protein families
73. A map of the protein space-an automatic hierarchical classification of all protein sequences