geoscience.net logo
+ Resolve Article
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter

+ Translate
+ Subscribe to Site Feed
GeoScience Most Shared ContentMost Shared Content

Identification and classification of protein fold families


, : Identification and classification of protein fold families. Protein Engineering 6(5): 485-500

We have developed a method for identifying fold families in the protein structure data bank. Pairwise sequence alignments are first performed to extract families of homologous proteins having 35% or more sequence identity. Representatives are selected with the best resolution and R-factor to give a nonhomologous data set. Subsequent structure comparisons between all members of this set detect homologous folds with low sequence identity but highly conserved structures. By softening the requirement on structural similarity, families of analogous proteins are obtained that have related folds but more diverse structures. Representatives are selected to give a non-analogous data set. Starting with 1410 chains from the Brookhaven Data Bank, we generate a set of 150 nonhomologous folds and a set of 112 non-analogous folds. Analysis of sequence and structure conservation within the larger families shows the globins to be the most highly conserved family and the TIM barrels the most weakly conserved.

US$19.90

PMID: 8415576

DOI: 10.1093/protein/6.5.485


Other references

Vincent, T., 1986: Les goelands argentes (Larus argentatus), leur expansion en centre-ville et les moyens de lutte permettant de s'y opposer. Bulletin Trimestriel de la Societe Geologique de Normandie et des Amis du Museum du Havre. 1985 ; 721-2: 79-89

Richert, D.A.; Westerfeld, W.W., 1951: Xanthine oxidases in different species. The enzyme present in bird tissues was a dehydrogenase rather than an oxidase, since the aerobic activity of the enzyme was negligible in comparison with its activity in the presence of methylene blue. The enzyme present in mammalian tissues was a...

Wicks, T., 1977: Tolerance to benzimidazole fungicides in blue mold penicillium expansum on pears. A strain of P. expansum tolerant in vitro to benomyl, thiophanate-methyl, and thiabendazole was isolated from pears which were dipped in benomyl 4 mo. previously. Mold was not controlled when pears, inoculated with the tolerant strain, were dipped...

Godel V.; Regenbogen L.; Lazar M.; Coscas G., 1980: Vascular accidents in preretinal arterial loops. Patients (3) with preretinal arterial loops complicated by obstructive accidents of various intensities are reported. The range of the complication varied from arterial spasm to transient retinal hemorrhages and arterial branch occlusion with perm...

Anonymous, 2003: Mayo Clinic office visit. Testosterone and women. Mayo Clinic Women's Healthsource 5(2): S1-S2

Hauri H.P.; Naim H.; Roth J.; Sterchi E., 1987: Sucrase isomaltase deficiency in man different mutations disrupt intracellular transport and function of an intestinal microvillar hydrolase. Journal of Cell Biology 105(4 PART 2): 59A

Rozendal R.H.; Veeger H.E.; Van Der Helm F.C.T.; Pronk G.M.; Van Der Woude L.H., 1989: Modelling of the shoulder mechanism. Journal of Biomechanics 22(10): 1076

Lai, Y.T.; Masker, W., 1998: In vitro repair of gaps in bacteriophage T7 DNA. An in vitro system based upon extracts of Escherichia coli infected with bacteriophage T7 was used to study the mechanism of double-strand break repair. Double-strand breaks were placed in T7 genomes by cutting with a restriction endonuclease whic...

Takahashi, T.; Nakamura, H., 1994: Roles of electrostatic interaction in molecular recognition. Tanpakushitsu Kakusan Koso. Protein, Nucleic Acid, Enzyme 39(7): 1059-1065

van Niekerk, L.J.; Espley, A.J., 1992: Goal posts in total hip replacement: a pelvic alignment device. Journal of the Royal College of Surgeons of Edinburgh 37(4): 271-271