The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths and weaknesses that need to be highlighted. We compared and presented results ofsix most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.

The study of gene GJB2/DFNB1 causing deafness in humans by linkage analysis from district Peshawar.

Families with at least 2 or more individuals having hereditary hearing loss were enrolled from different areas of Khyber Pakhtoonkhwa, mainly from district Peshawar. Detailed history was taken from each family to minimize the presence of other abnormalities and environmental causes for deafness. Families were questioned about skin pigmentation, hair pigmentation, and problems relating to balance, vision, night blindness, thyroid, kidneys, heart, and infectious diseases like meningitis, antibiotic usage, injury, and typhoid. The pedigree structures were based upon interviews with multiple family members, and pedigrees of the enrolled families were drawn using Cyrillic program (version 2.1). All families showed recessive mode of inheritance. I studied 8 families of these 10. For linkage analyses, studies for DFNB1 locus, 3 STR markers (D13S175, D13S292, and D13S787) were genotyped using polyacrylamide gel electrophoresis (PAGE) and haplotypes were constructed to determined, linkage with DFNB1 locus. From a total of 8 families, a single family-10 showed linkage to DFNB1 locus.

Molecular investigation of mental retardation locus gene PRSS12 by linkage analysis.

The present study was carried out to determine the prevalence of families having mental retardation in Pakistani population. We enrolled seven mentally retarded (MR) families with two or more affected individuals. Family history was taken to minimize the chances of other abnormalities. Pedigrees were drawn using the Cyrillic software (version 2.1). The structure of pedigrees shows that all the marriages are consanguineous and the families have recessive mode of inheritance. All the families were studied by linkage analysis to mental retardation locus (MRT1)/gene PRSS12. Three STR markers (D4S191, D4S2392, and D4S3024) in vicinity of mental retardation (MR) locus (MRT1)/gene PRSS12 were amplified on all the sample of each family by PCR. The PCR products were then genotyped on non denaturing polyacrylamide gel electrophoresis (PAGE). The Haplotype were constructed to determine the pattern of inheritance and also to determine that a family was linked or unlinked to gene PRSS12. One out of the seven families was potentially linked to gene PRSS12, while the other six families remain unlinked.

Expression and identification of folate-sensitive fragile sites in British Suffolk sheep (Ovis aries).

An investigation to understand the dynamics and biological significance of fragile site expression, and identification of 5-fluorodeoxyuridine (FUdR) induced chromosomal gaps/breaks, were carried out in an experimental flock of 45 Suffolk sheep. The statistical comparison revealed, highly significant variation in the frequency of chromosomal fragile site expression between control and FUdR cultures. Mean (+/- S.D.) values for cells with gaps and breaks, or aberrant cell count (AC), and the number of aberrations (NoA) per animal were 2.02 +/- 0.34, 2.42 +/- 0.48, 13.26 +/- 0.85 and 21.87 +/- 1.88 (P lessthan 0.01) in control and FUdR cultures, respectively. The comparison of age revealed nonsignificant variation between control and FUdR cultures. The G-band analysis of fragile site data revealed gaps in 29 autosomal and two X-chromosomal bands in the control cultures, whereas FUdR treated cultures scored 78 unstable bands in autosomes of which 56 were significantly fragile. X-chromosomes expressed breaks and gaps in six G-negative bands and five of them (Xq13, Xq15, Xq17, Xq24 and Xq26) were significantly fragile. The distribution comparison of autosomal fragile sites between sex groups did not reveal any significant variation. Female X-chromosomes were significantly more fragile than the male X-chromosomes. The distribution comparison for age groups (lambs versus adults) revealed significantly higher number of fragile bands in adults. Comparison of published data on reciprocal translocations in sheep with the fragile-site data obtained in this study indicated that the break sites of both phenomena were correlated. Similarities were also found between fragile sites and breakpoints of evolutionary significance in family Bovidae.