Volume 1 Issue 1
Short Research Article
Combinatorial Ligand Design from a Pool of Peptide Fragments
Christopher H. Schlitt, Arthur M. Lesk*
The binding of small molecules to proteins is in many cases an essential feature of the mechanisms of their function. Drugs that bind proteins allow us to modify or control these functions. Both for identification of the protein function, and for design of drugs that target proteins, it is useful to have computational methods that identify potential ligands to a protein of known structure. This is true despite the fact that ligand-induced conformational changes may degrade the quality of a ligand prediction, perhaps even fatally.
Short Research Article
Comparison of Cluego and Impala for Integrated Pathway Enrichment Analysis
Akshay Bhat, Vera Jankowski, Antonia Vlahou, Harald Mischak, Jerome Zoidakis*
High-throughput experimental technologies ranging from genomic sequencing and gene/protein profiling are now commonly being used for the molecular characterization of diseases. These techniques produce large datasets of differentially expressed features that include genes, mRNAs, proteins and metabolites. The abundant data defy straightforward intuitive interpretation. Hence the correlation of molecular features to biological pathways may ultimately help in understanding the patho-physiology of a disease.
Two Hypothetical Proteins from Bacillus thuringiensis Genomes were Parasporinlike Proteins
Parasporins are a group of anti-cancer proteins from Bacillus thuringiensis that preferentially kill cancer cells leaving the normal cells unaffected. Two hypothetical proteins were found from B. thuringiensis genomes to be homologous to Parasporin-2. Their structures were both β-sheet-dominant one with 4 α-helix occurred only in domain I, which were also seen in Parasporin-2. An aromatic cluster in domain I of the two proteins might serve as the binding site for target cells’ receptors as reported for Parasporin-2.
Systems Biology of the Proteomic Analysis of Cytotoxic Gold Compounds in A2780 Ovarian Cancer Cell Line: A Network Analysis
Tania Gamberi, Francesca Magherini, Tania Fiaschi, Elisa Valocchia, Giovanni Raugei, Pietro A. Modesti, Luigi Messori and Alessandra Modesti*
Gold and ruthenium compounds hold today great promise as new metallodrugs for treatment of human ovarian carcinoma; yet, their mode of action is still largely unknown. To shed light on their molecular mechanisms in previous studies we performed proteomic analysis in the A2780 human ovarian cancer cell line, after treatment with four different gold and two ruthenium compounds. To gain a better interpretation of their cellular effects we reported here the bioinformatic analysis of proteomic data that confirmed the action of these metallodrugs on previously identified signaling pathways such as glucose metabolism, protein folding, and cell division cycle and apoptosis.
From Oncogenetic Pedigrees to Family Profiles: A Necessary Step to Enable Statistics
Arbre M, Kwiatkowski F*, Serlet L, Bignon YJ*
Currently, with the progress of genetic research, more and more predispositions to hereditary diseases are discovered. As pangenomic analysis (genome-wide screening) cannot be realized routinely – partly for ethical reasons – it is necessary to predict which genes are the most likely to be mutated and then perform targeted genomic analysis.In the oncogenetic routine, pedigrees are frequently used to diagnose hereditary predispositions. These contain two kinds of data: first the genealogy, i.e. the relations between members from which for example fertility and mortality parameters can be calculated and second, possible clinical information that may characterize the phenotype of a hereditary predisposition to a disease.
In Silico Analysis and 3d Structure Prediction of mitochondrial RHO GTPase 2 Protein of Danio rerio (zebra fish) by Homology Modeling
Rumpi Ghosh, A.D. Upadhayay, A.K. Roy* and Mamta Singh
The present study deals with Insilco characterization of homology-dependent modeling and 69739.7 kDa Mitochondrial RHO GTPase proteins of Danio;rerio (Brachydanio rerio) not attempted earlier for this species. The secondary structure prediction reveals the extended 43 coil Regions, 24 helix region, and 13 strands. The 3D structure of this protein was generated using Deep view/Swiss PDB viewer 3.7 by homology modeling. The predicted 3D model showed that 88.1% residues fall in the most favored region, 11.3% in additional allowed region, 0.6% generously allowed region and 0% fall in the disallowed region.