Statistics of sequence-structure threading

Current Opinion in Structural Biology

Volumn 5, Issue 2, 1995, Pages 236-244

  Bryant, Stephen H ^a   Altschul, Stephen F ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; GENETIC PROCEDURES; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW; STATISTICS;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, FACTUAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SUPPORT, U.S. GOV'T, P.H.S.;

EID: 0029008017     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/0959-440X(95)80082-4     Document Type: Article

References (73)

1. Statistical methods and insights for protein and DNA sequences
2. Issues in searching molecular sequence databases
3. Sensitive methods for determining the relatedness of proteins with limited sequence homology
4. Catching a common fold
5. Inverted protein structure prediction
6. New programs for protein tertiary structure prediction
7. De novo and inverse folding predictions of protein structure and dynamics
8. Protein fold recognition
9. Structure prediction of proteins — where are we now?
10. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
11. Generating and testing protein folds
12. The relation between the divergence of sequence and structure in proteins
13. One thousand families for the molecular biologist
14. Ancient conserved regions in new gene sequences and the protein databases
15. A method to identify protein sequences that fold into a known three-dimensional structure
16. A new approach to protein fold recognition
17. Topology fingerprint approach to the inverse folding problem
18. An empirical energy function for threading protein sequence through folding motif
19. In search of protein folds
20. A proposed structural model of domain 1 of fasciclin III neural cell adhesion protein based on an inverse folding algorithm
21. Eukaryotic translation elongation factor 1γ contains a glutathione transferase domain — study of a diverse, ancient protein superfamily using motif search and structure modeling
22. Protein structural similarities predicted by a sequence-structure compatibility method
23. Three-dimensional profiles from residue-pair preferences: identification of sequences with β/α-barrel fold
24. Identification of common molecular subsequences
25. Improved tools for biological sequence comparison
26. Basic local alignment search tool
27. A Phase Transition for the Score in Matching Random Sequences Allowing Deletions
28. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
29. Strong Limit Theorems of Empirical Functionals for Large Exceedances of Partial Sums of I.I.D. Variables
30. Strong Limit Theorems of Empirical Distributions for Large Segmental Exceedances of Partial Sums of Markov Variables
31. Applications and statistics for multiple high-scoring segments in molecular sequences
32. An Extreme Value Theory for Sequence Matching
33. The Erdos-Renyi Strong Law for Pattern Matching with a Given Proportion of Mismatches
34. The statistical distribution of nucleic acid similarities
35. A nonlinear measure of subalignment similarity and its significance levels
36. The significance of protein sequence similarities
37. Maximum-likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores
38. Rapid and accurate estimates of statistical significance for sequence database searches
39. Analysis of gene duplication repeats in the myosin rod
40. A general method applicable to the search for similarities in the amino acid sequences of two proteins
41. Matching sequences under deletion-insertion constraints
42. On the Theory and Computation of Evolutionary Distances
43. Probabilistic behavior of longest-common-subsequence length
44. On the statistical assessment of similarities in DNA sequences
45. Random sequences
46. Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage
47. Recognition of distantly related proteins through energy calculations
48. A search for the most stable folds of protein chains
49. Contact potential that recognizes the correct folding of globular proteins
50. Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures
51. Protein tertiary structure recognition using optimized Hamiltonians with local interactions.
52. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds
53. Alignment and searching for common protein folds using a data bank of structural templates
54. A structural basis for sequence comparisons: an evaluation of scoring methodologies
55. Hamiltonians for protein tertiary structure prediction based on three-dimensional environment principles
56. Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies
57. Prediction of protein structure by evaluation of sequence-structure fitness Aligning sequences to contact profiles derived from three-dimensional structure
58. The three-dimensional profile method using residue preference as a continuous function of residue environment
59. Correctly folded proteins make twice as many hydrophobic contacts
60. Identification of native protein folds amongst a large number of incorrect models The calculation of low energy conformations from potentials of mean force
61. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein comformations
62. Recognition of errors in three-dimensional structures of proteins
63. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
64. A branch and bound algorithm for optimal protein threading with pairwise (contact potential) amino acid interactions
65. Information enhancement methods for large scale sequence analysis
66. Non-globular domains in protein sequences: automated segmentation using complexity numbers
67. De novo protein design using pairwise potentials and a genetic algorithm
68. Empirical and structural models for insertions and deletions in the divergent evolution of proteins
69. Sequence alignment and penalty choice
70. The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions
71. Protein data bank
72. Searching protein structure databases has come of age