Algorithms for prediction of α-helical and β-structural regions in globular proteins

Lim, V.I.

doi:10.1016/0022-2836(74)90405-7

Cited by 465 publications

(177 citation statements)

References 26 publications

Supporting

Mentioning

169

Contrasting

Unclassified

Order By: Relevance

“…For example, at aligned position 74, Wilmot and Thornton [23] predict involvement in a turn for hTPO, pTPO and hMPO whilst Rose [24] predicts turn for hTPO and pTPO; a total of 5/6 predictions for turn. At the same position, Lim [25] predicts hMPO as ~, Robson [27] predicts hTPO and pTPO as fl, and hMPO as a, whilst Chou and Fasman [26] predict hTPO and hMPO as a. Thus, a and fl are equally predicted 3/9 at this position, by default, coil is predicted 3/9, whilst turn is predicted 5/6.…”

Section: Sequence Alignmentmentioning

confidence: 89%

“…Turns were predicted using (i) the method of Wilmot and Thornton [23] (Program supplied by Dr C. Wilmot) and (ii) that of Rose [24]. a-Helix and B-strand regions were predicted using the algorithms of Lim [25], Chou and Fasman [26] and Robson [27] as programmed in the Leeds prediction suite (Dr. E. Eliopoulos, Department of Biophysics, University of Leeds, Leeds, UK). The results of the alignment and annotated predictions were formatted using the HOMED programme (Dr P.A.…”

Section: Alignment Of Sequences and Prediction Techniquesmentioning

confidence: 99%

“…a total of 6 predictions at each position, were combined by expressing the number of predictions that define each residue as part of a turn as a fraction of the total possible number of predicted turns. Similarly, predic- tions of helix, strand and coil were combined for the 9 predictions (Lim [25], Chou and Fasman [26] and those of Robson [27] on each of the 3 sequences) at each position.…”

Section: Sequence Alignmentmentioning

confidence: 99%

See 2 more Smart Citations

Prediction of domain organisation and secondary structure of thyroid peroxidase, a human autoantigen involved in destructive thyroiditis

et al. 1990

View full text Add to dashboard Cite

Organ specific autoimmune diseases are relatively common immunological disorders in man which include thyroid autoimmune disease, insulindependent diabetes mellitus and myasthenia gravis. The target autoantigens in some of these diseases have recently been characterised. In thyroid autoimmune disease this includes the key enzyme, thyroid peroxidase (TPO), which is involved in the generation of thyroid hormone. Structural knowledge about autoantigens such as thyroid peroxidase will allow a greater understanding of the interaction between autoantigens and the aberrant immune response, and facilitate the development of strategies for antigen-specific therapeutic manipulation. We report here a prediction of the secondary structure of thyroid peroxidase, together with the results of circular dichroic spectroscopy of a homologous purified enzyme. A combination of 3 secondary structure prediction programs has been used, following multiple sequence alignment, and TPO has been found to consist mainly of ~t-helical conformation, with little p-sheet present. This structure prediction, together with knowledge of the exon-intron boundaries allows a model for the domain organisation of the TPO molecule to be proposed.

show abstract

Section: Sequence Alignmentmentioning

confidence: 89%

Section: Alignment Of Sequences and Prediction Techniquesmentioning

confidence: 99%

Section: Sequence Alignmentmentioning

confidence: 99%

See 1 more Smart Citation

Prediction of domain organisation and secondary structure of thyroid peroxidase, a human autoantigen involved in destructive thyroiditis

et al. 1990

View full text Add to dashboard Cite

show abstract

“…Application of his algorithm [6] to the amino acid sequence of protein L25 predicts two a-helical regions, 4-12 and 53-69, and four/3-structural region, 28-32, 38-42, 46-50 and 89-93. This localization of the regular secondary structure was taken as the zero approximation in constructing the model of the tertiary structure and was varied when necessary to obtain the optimum folding according to our criteria.…”

Section: The Secondary Structurementioning

confidence: 99%

Prediction of the three‐dimensional structure for ribosomal protein L25

1975

View full text Add to dashboard Cite

“…arBlnine-39 refers to the highly conserved arglnine within the human sr¢ FLVRES sequenge), Secondary structure predictions were obtained by combining the results of five predictive algorithms applied independently to each aligned sequence. Helix and strand predictions were performed by ¢ombininB the methods of Lira [14], Chou and Faro'nan [i 5] and Robson [16], whilst the methods of Rose [17] and Wllmot and Thornton [18] were used to predict turns. The combination of methods was performed as described in 13saga et al [19].…”

Section: Introduction Ences May Not Be Made Through Homology Modellinmentioning

confidence: 99%

Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains

1992

View full text Add to dashboard Cite

Src homology 2 (SH2) regions arc short (approximately 100 amino acids), non-catalytic domains conserved among a wide variety of proteins involved in cytoplasmic signaling induced by growth factors. It is thought that SHZ domains play an important role in the intracellular response to growth faclor stimulation by binding to phosphotyrosinc containing proteins, In this paper WC apply the techniques of multiple scqucnce alignment, secondary structure prediction and conservation analysis to 67 SH2 domain amino acid sequences. This combined approach predicts seven core secondary structure regions with the pattern /3-a-~-/%&%, identifies those residues most likely to be buried in the hydrophobic core of the native SH2 domain, and highlights patterns of conservation indicative of secondary structural elements. Rcsiducs likely to be involved in phosphotyrosine binding arc shown and orientations of the predicted secondary structures suggested which could enable such residues to cooperate in phosphate hinding. WC propose a consensus pattern that encapsulates the principal conserved features of the SH2 domains. Comparison of the proposed Sli2 domain of ukr to this pattern shows only 12140 matches, suggesting that this domain may not exhibit SH2-like properties.

show abstract

Algorithms for prediction of α-helical and β-structural regions in globular proteins

Cited by 465 publications

References 26 publications

Prediction of domain organisation and secondary structure of thyroid peroxidase, a human autoantigen involved in destructive thyroiditis

Prediction of domain organisation and secondary structure of thyroid peroxidase, a human autoantigen involved in destructive thyroiditis

Prediction of the three‐dimensional structure for ribosomal protein L25

Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains

Contact Info

Product

Resources

About