An HMM model for coiled-coil domains and a comparison with PSSM-based predictions

Bioinformatics

Volumn 18, Issue 4, 2002, Pages 617-625

  Delorenzi, Mauro ^a   Speed, Terry ^a  

^a WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; AMINO ACID;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER PROGRAM; GENETICS; GENOME; INFORMATION RETRIEVAL; METHODOLOGY; MOLECULAR GENETICS; PROBABILITY; PROTEIN CONFORMATION; PROTEIN DATABASE; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; STATISTICAL MODEL; VALIDATION STUDY; AMINO ACID ANALYSIS; AUTOMATION; CONTROLLED STUDY; FREQUENCY ANALYSIS; GENOMICS; INTERMETHOD COMPARISON; MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; VALIDATION PROCESS;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; GENOME; INFORMATION STORAGE AND RETRIEVAL; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 0035999986     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.4.617     Document Type: Article

References (40)

1. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
2. Hidden Markov models of biological primary sequence information
3. An equality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes
4. Neural Networks for Speech and Sequence Recognition
5. An iterative method for improved protein structural motif recognition
6. Predicting coiled coils by use of pairwise residue correlations
7. The protein data bank
8. Computational approaches to identify leucine zippers
9. Heptad breaks in alpha-helical coiled coils: Stutters and stammers
10. The packing of alpha-helices: Simple coiled-coils
11. Biological Sequence Analysis
12. Multiple alignment using hidden Markov models
13. Maximum discrimination hidden Markov models of sequence consensus
14. Springs and zippers: Coiled coils in SNARE-mediated membrane fusion
15. Amino acid substitution matrices from protein blocks
16. Coiled-coil assembly by peptides with non-heptad sequence motifs
17. Predicting leucine zipper structures from sequence
18. Hidden Markov models for sequence analysis: Extension and analysis of the basic method
19. Hidden Markov models in computational biology. Applications to protein modeling
20. Hidden neural networks
21. Helix capping in the GCN4 leucine zipper
22. Coiled coils: New structures and new functions
23. Prediction and analysis of coiled-coil structures
24. Predicting coiled-coil regions in proteins
25. Predicting coiled coils from protein sequences
26. A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae
27. Coiled-coils in alpha-helix-containing proteins: Analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins
28. Position dependence of amino acid intrinsic helical propensities II: Non-charged polar residues: Ser, Thr, Asn, and Gln
29. A tutorial on hidden Markov models and selected applications in speech recognition
30. Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol
31. Mechanisms of intracellular protein transport
32. LearnCoil-VMF: Computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins
33. Computational learning reveals coiled coil-like motifs in histidine kinase linker domains
34. Coiled coils in both intracellular vesicle and viral membrane fusion
35. Identification of common molecular subsequences
36. Determination of alpha-helix N1 energies after addition of N1, N2, and N3 preferences to helix/coil theory
37. Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 A resolution
38. Socket: A program for identifying and analysing coiled-coil motifs within protein structures
39. MultiCoil: A program for predicting two- and three-stranded coiled coils
40. Predicting oligomerization states of coiled coils