Protein engineering is an important tool for overcoming the limitations of natural enzymes as biocatalysts. In this regard computational Tools are becoming increasingly important in order to create improved or novel enzymes. We developed a useful collection of Bioinformatics Tools in protein engineering. These applications are freely available at http: //bioinf.modares.ac.ir. A short description will come in the following: PUTracer is a useful and easy to use web based application to assign number of domains and domain boundaries in a protein. Recognition of domains in proteins is a critical step in chimeric protein engineering. LinDa (Linker Design Assistant) is a database of protein fragments in 4-20 amino acid length. Linda is an effective tool to chimeric protein engineering and peptide design. MPDB (Mutation Proposer on Disulfide Bond): Disulfide bonds formation is one of the solutions to increase the thermal stability of enzymes. MPDB gives a list of amino acids pair with potential to form a disulfide bond. CFinder (Contact Finder) Accurate identification of amino acids involved in the binding of the two proteins has wide applications, including antibody optimization, analysis of docking studies, increasing protein stability and peptide design. CFinder identifies amino acids involved in binding in a protein complex and also an individual amino acid neighbors too. Mini Mutate is a user friendly application to have the structure of a mutated protein. The input of application is native protein structure in PDB format and desired mutation. It will give the mutated protein structure after replacing amino acid and optimizing the structure.

Chemodiversity in plants provides sources of great value which might be helpful for finding new leads in drug discovery programs. Fabaceae as the third largest family of flowering plants was chosen to investigate its possible antifungal activity. In order to increase the effectiveness of the result, molecular similarity methods and chemical data were used. Twelve plants were selected from Fabaceae and collected from the North and South of Iran. Percolation method with 80% ethanol was used for extraction of collected plants. Antifungal activities of these extracts were determined using broth microdilution method against Candida albicans (C. albicans) ATCC 10231, Aspergillus fumigatus (A. fumigatus) AF 293 and Asperigillus niger (A. niger) ATCC 16404. Extracts with promising activity were screened for toxicity with larvae of Artemia salina (brine shrimp). Dalbergia sissoo, Lathyrus pratensis, Oreophysa microphyalla, Astragalus stepporum, Ebenus stellata, Sophora alopecuroides, Ammodendron persicum and Taverniera cuneifolia showed activity against at least one of the microorganisms used in this study. According to the results of our experiment, the extracts of these plants can be used for further investigation in therapeutic research.

Background: MicroRNAs (miRNAs) are small endogenous non-coding RNAs with fundamental roles in the regulation of protein expression that is involved in the pathogenesis of many cancers including breast cancer. Among them is miR-206, whose role as a tumor suppressor gene has been demonstrated in breast cancer. Consequently, the identification of its putative target in breast cancer is of practical value. Methods: In the present study, we have suggested a new approach for the identification of miR-206 target genes with possible role in breast cancer pathogenesis. We used 15 online Tools for the prediction of miR-206 target genes as well as gene expression data produced by DNA microarray technology. Results: By combining these two sets of data, we suggested a list of miR-206 target genes with possible involvement in breast cancer. In addition, we depicted an interaction network including miR-206 and its putative targets. Conclusions: Considering the complexity of miR-206 interactions with several targets, such in silico analyses would considerably lessen the work load of laboratory experiments.

Prolactin is mainly secreted by the anterior pituitary and is able to stimulate mammary gland development and lactation in mammalians. Although prolactins share a common ancestral gene encoding, they show species specific characteristics and their efficiency may be different in various mammals. The importance of protein structures of all sequences of this hormone have been studied by various Bioinformatics algorithms. The results showed Bioinformatics Tools and modeling methods can be used to identify the species specificity of prolactin hormones in animals with an acceptable precision rate. Based on the author’s knowledge, this is the first report on the structural variation of prolactin hormones by specific structural protein features. Gain ratio model acquired the best accuracy and performance among the algorithms applied here and can be used on similar proteins. The counts and the frequencies of dipeptides were the most important protein attributes in this regard. It has also been reported here that feature selection or attribute weighting can be used to select the most important protein attributes and to reduce the burden of processing equipment. The new findings presented here open up new windows in understanding the characteristics of prolactin hormones and also pave the way to engineer more efficient hormones by using various mutagenesis Tools such as site directed mutagenesis.

Introduction. Activation of the complement system following transplantation may result in allograft rejection. Our study aimed to evaluate the potential relationship between factors affecting kidney transplant success and complement 5 (C5) using bioinformatic Tools. Methods. GenCards and Genemania were used to provide the genetic functional information belonging to the C5 gene, and genomic browsers of STRING, UCSC, KEGG were used to reveal interactions with other genes and various pathways. MiRDB was used to specify the miRNAs that were associated with the C5 gene. The UniProt database was used to determine the tissues that expressed the C5 gene using protein-protein interactions. Results. In the bioinformatic analyses performed, high levels of C5 gene expression were found in the naiive kidney. Twenty-five genes were found to be strongly associated with C5. Fifty-four miRNAs targeting the C5 gene were specified. The C5 gene was found to be involved in biologic processes such as complement activation (FDR = 6. 46e-22), complement binding (FDR = 2. 20e-06), cytolysis (FDR = 4. 82e-14), regulation of complement activation (FDR = 4. 08e-24), positive regulation of vascular endothelial growth factor production (FDR = 0. 0430), regulation of macrophage chemotaxis (FDR = 0. 0447), activation of the immune response (FDR = 1. 26e-13), leukocyte-mediated immunity (FDR = 1. 41e-09), innate immune response (FDR = 3. 05e-09), allograft rejection (FDR = 2. 40e-12), oxidative injury response (FDR = 0. 00016), and trigerring of the beginning of the complement cascade (FDR = 0. 0244). Conclusions. The data obtained in this study will be used to guide future experimental investigations in the field of transplantation, and these data will give physicians with insight into allograft status following transplantation.