Bio Saga Blog - A Chronicle of Life Sciences & Informatics

In structural biology, similarity analysis of protein structure is a crucial step in studying the relationship between proteins. Despite the considerable number of techniques that have been explored within the past two decades, the development of new alternative methods is still an active research area due to the need for high performance tools. Results: In this paper, we present TS-AMIR, a Topology String Alignment Method for Intensive Rapid comparison of protein structures. The proposed method works in two stages: In the first stage, the method generates a topology string based on the geometric details of secondary structure elements, and then, utilizes an n-gram modelling technique over entropy concept to capture similarities in these strings. This initial correspondence map between secondary structure elements is submitted to the second stage in order to obtain the alignment at the residue level. Applying the Kabsch method, a heuristic step-by-step algorithm is adopted in the secon...

Greetings from Department of Bioinformatics, Alagappa University It gives us immense pleasure to announce that the Department of Bioinformatics, Alagappa University, Karaikudi is organizing 4th National Symposium cum Workshop on “Recent Trends in Structural Bioinformatics and Computer Aided Drug Design [SBCADD’2012]” during Feb 20th – 23rd, 2012. The motive of the National symposium cum workshop is to provide theoretical and practical exposure of Structural Bioinformatics and Computer Aided Drug Design among academicians and technocrats in order to cater the industrial and academic need. We have invited eminent personalities from reputed organizations, who will enlighten the participants in the related fields. Please download the brochure containing information and registration details along with this invitation for your kind perusal. We extend humble invitation to you and your colleagues to participate actively in the workshop and make it a big success. It will be appreciated if you c...

Protein misfolding underlies many neurodegenerative diseases, including the transmissible spongiform encephalopathies (prion diseases). Although cells typically recognize and process misfolded proteins, prion proteins evade protective measures by forming stable, self-replicating aggregates. However, coexpression of dominant-negative prion mutants can overcome aggregate accumulation and disease progression through currently unknown pathways. Here we determine the mechanisms by which two mutants of the Saccharomyces cerevisiae Sup35 protein cure the [ PSI + ] prion. We show that both mutants incorporate into wild-type aggregates and alter their physical properties in different ways, diminishing either their assembly rate or their thermodynamic stability. Whereas wild-type aggregates are recalcitrant to cellular intervention, mixed aggregates are disassembled by the molecular chaperone Hsp104 . Thus, rather than simply blocking misfolding, dominant-negative prion mutants target multiple...

The Workshop Drug discovery is an expensive and time taking process and therefore new approaches based on chemoinformatics and bioinformatics are being adopted.The knowledge of the 3D structures of protein targets is now playing a major role at all stages of drug discovery. The distinct nature of biological and chemical information requires the integrated capabilities of both bioinformatics and chemo-informatics to decipher existing and hidden relationships. Bioinformatics and chemo-informatics have largely evolved independently from biology and chemistry. Cheminformatics is an inter-disciplinary subject of storage, processing and retrieval of chemical information. Bioinformatics and chemoinformatics have significantly assisted in lead optimization, fingerprinting, pharmacophore designing, target identification, QSAR and their application can lead to discovery of new molecules. Molecular modeling using 3D graphics and optimization techniques helps the scientists to understand how drug...

Belgian biotech firm Galapagos today announced its BioFocus service division has extended a contract with Amgen through 2012 to include target discovery and validation work. The extension will include the use of BioFocus' target discovery platform to deliver novel targets to support Amgen's therapeutic programs. Galapagos will receive €2 million ($2.6 million) in research fees in the first year, under the terms of the deal. It is also eligible for access fees and milestone payments. Originally forged in 2002, the collaboration between BioFocus, which Galapagos acquired in 2005, and Amgen involves identifying new molecules against drug targets. The partnership was extended in 2006 and 2008. BioFocus' discovery platform includes the use of  in vitro  and cell-based screening, structural biology, and chemogenomic and informatics tools.

Under the auspices of the University of Tübingen, approximately 120 students from all over the world are working on their PhDs at the Max Planck Institute for Developmental Biology and the Friedrich Miescher Laboratory. Here, they profit from an interdisciplinary environment and first-rate scientific resources. Dedicated support and educational programs foster the scientific growth of doctoral students. The program offers cutting edge training in Bioinformatics Structural Biology Plant & Animal Development  Molecular & Cellular Biology/ Biochemistry Developmental & Quantitative Genetics Evolutionary Biology & Ecological Genetics The  application deadline is November 24, 2010. Do you wish to know more?

BioFocus DPI has partnered with the cancer drug candidate and biomarker company Oncodesign to offer an integrated service platform, Galapagos division BioFocus DPI said today. The agreement will create a service that combines BioFocus DPI's target discovery and screening capabilities with Oncodesign's biomarker and pharmacological services to offer target validation and clinical candidate selection services, the company said. BioFocus DPI offers gene-to-drug candidate discovery services, including in vitro and cell-based screening, chemogenomic and informatics offerings , storage, distribution, and other structural biology and medicinal chemistry services. XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "manually" annotated facts from PubMed on a weekly basis Innovative Features like Semantic Search , Concept Linking , Bibliographic search , Save, ...

Protein domains are the structural and functional units of proteins. The ability to parse proteins into different domains is important for effective classification, understanding of protein structure, function, and evolution and is hence biologically relevant. Several computational methods are available to identify domains in the sequence. Domain finding algorithms often employ stringent thresholds to recognize sequence domains. Identification of additional domains can be tedious involving intense computation and manual intervention but can lead to better understanding of overall biological function. In this context, the problem of identifying new domains in the unassigned regions of a protein sequence assumes a crucial importance. Accumulation of domain information of sequence homologues can substantially aid prediction of new domains. In this paper, we propose a computationally intensive, multi-step bioinformatics protocol as a web server named as PURE (Prediction of Unassigned REg...

Already blogging about vital information that can be obtained form publications and scientific literature Smart tools to track, analyze and visualize research and the importance of Protein structure information in Protein structure databases with new web services for structural biology and biomedical research . Now one of the tactics used by influenza virus to take over the machinery of infected cells has been laid bare by structural biologists at the European Molecular Biology Laboratory ( EMBL ) and the joint Unit of Virus Host-Cell Interaction of EMBL, the University Joseph Fourier and National Centre for Scientific Research (CNRS), in Grenoble, France. The high-resolution image of the influenza virus' PB2 protein shows how the virus steals a 'cap' molecule from its host to take over the protein production machinery and multiply. PB2 binds the cap by sandwiching it between aromatic amino acids. "Viruses are masters of cunning when it comes to hijacking the normal f...

Heart attacks are commonly caused by blood clots formed of blood platelets. A new research suggests that it should be possible to create a clot-busting pill that targets a receptor on the blood cells’ surface, something that high-risk patients could take at the first sign of chest pain. The key to such a pill is according to the research findings a receptor called αIIbβ3 on the platelets’ surface that is intimately involved in the aggregation process. Interfering with αIIbβ3 can prevent an unwanted thrombus and the three αIIbβ3 inhibitors currently on the market can do just that. But they also have side effects and risks and must be administered intravenously. Researchers at Rockefeller University have found a new molecule, called RUC-1 , that not only appears to sidestep these problems but, unlike existing drugs, could be taken orally.

The Protein Data Bank Japan (PDBj) curates , edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes 25–30% of all deposited data in the world. Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases. Several applications have been developed at PDBj for structural biology and biomedical studies : (i) a Java-based molecular graphics viewer, j V; (ii) display of electron density maps for the evaluation of structure quality; (iii) an extensive database of molecular surfaces for functional sites, e F-site, as well as a search service for similar molecular surfaces, e F-seek; (iv) identification of sequence and structural neighbors; (v) a graphical user interface to all known protein folds with links to the above applications, Protein Globe. Recent examples are shown that highlight the...