TM Finder: A prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales

Protein Science

Volumn 10, Issue 1, 2001, Pages 212-219

  Deber, Charles M ^a,b   Wang, Chen ^a,b   Liu, Li Ping ^a,b   Prior, Andrew S ^a   Agrawal, Shuchi ^a   Muskat, Brenda L ^a   Cuticchia, A Jamie ^a  

^a HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Membrane protein prediction; Nonpolar phase helicity; Threshold hydrophobicity; TM Finder; Transmembrane segments

Indexed keywords

GLOBULAR PROTEIN; MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROPHILICITY; HYDROPHOBICITY; MOLECULAR MIMICRY; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; HUMANS; MEMBRANE PROTEINS; MODELS, CHEMICAL; PROTEIN CONFORMATION; SOFTWARE;

EID: 0035104092     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.30301     Document Type: Article

References (21)

1. Empirical predictions of protein conformation
2. X-ray structure analysis of a membrane protein complex. Electron density map at 3 Å resolution and a model of the chromophores of the photosynthetic reaction center from R. viridis
3. The structure of the potassium channel: Molecular basis of K+ conduction and selectivity
4. Analysis of membrane and surface protein sequences with the hydrophobic moment plot
5. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
6. Cloning of full-length elastin cDNAs from a human skin fibroblast recombinant cDNA library: Further elucidation of alternative splicing utilizing exon-specific oligonucleotides
7. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy
8. Reversed-phase liquid chromatography as a useful probe of hydrophobic interactions involved in protein folding and protein stability
9. A simple method for displaying the hydropathic character of a protein
10. A measure of helical propensity for amino acids in membrane environments
11. Guidelines for membrane protein engineering derived from de novo designed model peptides
12. Uncoupling hydrophobicity and helicity in transmembrane segments: α-helical propensities of the amino acids in nonpolar environments
13. Combining hydrophobicity and helicity: A novel approach to membrane protein structure prediction
14. Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: Comparison with experimental scales
15. Solution structure of the M13 major coat protein in detergent micelles: A basis for a model of phage assembly involving specific residues
16. Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins
17. Light-induced structural changes in photosynthetic reaction center: Implications for mechanism of electron-proton transfer
18. The whole structure of the 13-subunit oxidized cytochrome C oxidase at 2.8 Å
19. Helicity of hydrophobic peptides in polar vs. non-polar environments
20. δ-Regions in proteins: Helices mispredicted as transmembrane segments by the threshold hydrophobicity requirement
21. Experimentally determined hydrophobicity scale for proteins at membrane interfaces