the automatic assignment of protein secondary structure from three dimensional coordinates is an essentialstep in the characterization of protein structure.although, the recognition of secondary structures suchas alpha-helices and beta-sheets seem straightforward, but there are many different definitions, eachregarding different criteria. we have developed a newalgorithm for protein helix assig...

background: genomic dna was isolated from parabronema skrjabini . rrna region was amplified and sequenced. methods : the rna secondary structure was predicted using mfold software (http://mfold.rit.albany.edu). the secondary structure with bulge, hairpins, helices, interior, external and multi loops was predicted for 5.8srdna of our sequence of p. skrjabini and a sequence of p. skrjabini and tw...

background: formation of secondary structure such as dna hairpins or loops may influence molecular genetics methods and pcr based approaches necessary for genetic engineering, in addition to gene regulation. materials and methods: a polymerase chain reaction with splice overlap extension (soe-pcr) was used to create fully synthetic 1f5 chimeric anti-cd20 heavy- and light-chain genes. the chimer...

The automatic assignment of protein secondary structure from three dimensional coordinates is an essential step in the characterization of protein structure. <span style="font...

background: the phylogenetic location of chinese spirometra sparganum isolates remains unclear. the aim of this study was to explore the phylogenetic location of the spirometra sparganum isolates from china. methods: the 28s ribosomal dna (rdna) d1 sequences of 14 spirometra sparganum isolates collected from thirteen locations in china were analyzed by using neighbor-joining (nj), maximum parsi...

background: rna molecules play many important regulatory, catalytic and structuralroles in the cell, and rna secondary structure prediction with pseudoknots is one themost important problems in biology. an rna pseudoknot is an element of the rna secondary structure in which bases of a single-stranded loop pair with complementary basesoutside the loop. modeling these nested structures (pseudokno...

objectives the overall goal of this study was to carry out a set of comparative analyses of arsr gene in plasmid r773 and bacterial chromosome from escherichia coli bl-21(de3). methods pdb and ncbi databases and chimera, mega4, clc main workbench software and 3d-jigsaw and embl-ebi servers were applied to perform this study. by using these software and servers, multiple analyses including deter...

in this study, the effect of the secondary structure of the protein on the acid strength of three structures of random (r), alpha helix (α) and beta sheet (b) were investigated theoretically. these structures are related to the cationic amino acids of histidine and lysine in the polypeptide chain of eight-glycine residue. computational methods at the hf, b3lyp, x3lyp and m05-2x levels in the ga...

Abstract Viroids are smallest, single-stranded, circular, highly structured plant pathogenic RNAs that do not code for any protein. Viroids belong to two families, the Avsunviroidae and the Pospiviroidae. Members of the Pospiviroidae family adopt a rod-like secondary structure. In this study the most stable secondary structures of citrus viroid variants that reported from Fars province wer...