Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally- characterized transmembrane topologies

In Silico Biology

Volumn 2, Issue 1, 2002, Pages 19-33

  Ikeda, Masami ^a   Arai, Masafumi ^b   Lao, Demelo M ^b   Shimizu, Toshio ^b  

^a IWATE UNIVERSITY   (Japan)

^b HIROSAKI UNIVERSITY   (Japan)

Author keywords

Consensus prediction; Prediction performance assessment; Transmembrane protein database; Transmembrane proteins; Transmembrane topology prediction

Indexed keywords

MEMBRANE PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; EUKARYOSIS; EXPERIMENTAL MODEL; HUMAN; MEMBRANE COMPONENT; MEMBRANE MODEL; MEMBRANE STRUCTURE; METHODOLOGY; NONHUMAN; PREDICTION; PROKARYOTE; RELIABILITY; SEQUENCE ANALYSIS;

CELL MEMBRANE; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEINS; SOFTWARE;

EID: 0036132818     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (36)

1. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
2. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
3. Protein Information Resource: A community resource for expert annotation of protein data
4. The protein data bank
5. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III
6. Methods and algorithms for statistical analysis of protein sequences
7. TopPred II: An improved software for membrane protein structure predictions
8. Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method
9. The prediction of transmembrane protein sequences and their conformation: An evaluation
10. SOSUI: Classification and secondary structure prediction system for membrane proteins
11. TMbase - A database of membrane spanning proteins segments
12. Evaluation of transmembrane topology prediction methods by using an experimentally characterized topology dataset
13. MPtopo: A database of membrane protein topology
14. A model recognition approach to the prediction of all-helical membrane protein structure and topology
15. Prediction of membrane proteins based on classification of transmembrane segments
16. Prediction of secondary structure
17. The detection and classification of membrane-spanning proteins
18. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
19. A simple method for displaying the hydropathic character of a protein
20. The PSIPRED protein structure prediction server
21. A collection of well characterised integral membrane proteins
22. Evaluation of method for prediction of membrane spanning regions
23. Consensus predictions of membrane protein topology
24. A hierarchical artificial neural network system for the classification of transmembrane proteins
25. A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: The PRED-TMR algorithm
26. Prediction of membrane protein topology utilizing multiple sequence alignments
27. Transmembrane topology pattern and detection of transmembrane protein functions
28. CoPreTHi: A web tool which combines transmembrane protein segment prediction methods
29. Refining neural network predictions for helical transmembrane proteins by dynamic programming
30. Construction of a membrane protein database and an evaluation of several prediction methods of transmembrane segments
31. A hidden Markov model for predicting transmembrane helices in protein sequences
32. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
33. Principles governing amino acid composition of integral membrane proteins: Application to topology prediction
34. The HMMTOP transmembrane topology prediction server
35. Mitochondrial targeting sequences may form amphiphilic helices
36. Database resources of the National Center for Biotechnology Information