STRING - Search Tool for the Retrieval of Interacting Proteins

STRING is a database of known and predicted protein-protein interactions.The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:

• Genomic Context
• High-throughput Experiments
• (Conserved) Coexpression
• Previous Knowledge

STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently contains 1,513,782 proteins in 373 species.

Access STRING.

RNA Interference and Gene silencing

RNA interference, or RNAi, is a way for cells to regulate which genes would be expressed. This amazing phenomenon was first observed in petunias, when a scientist called Rich Jorgensen introduced a pigment-producing gene under the control of a powerful promoter. Instead of the expected deep purple color in the petunia, the result was a mixture of variegated and white petunias.RNAi was named the breakthrough of the year in 2002, yielding a new potential for disease treatment and unraveling the mysteries of the functioning of human genes.

So, why do we need to shutdown the production of some genes?

• Scientists have been interested in the ability to shut down genes, so that observing the effect of turning down a gene can be observed on an organism, giving clues about the function of the gene.
• The ability to shut off the genes, may also result in developing new treatments for diseases by turning down the harmful protein producing gene.

A very beautiful article about RNA Interference, or RNAi appeared on pbs.org, and can be found at http://www.pbs.org/wgbh/nova/sciencenow/3210/02.html.

Putting Playstation to work for science

A network of Playstation computers might help Danish scientists to solve themystery of prostate cancer.

A team of scientists has enlisted the help of Playstation 3 owners to help themcrack the code for prostate cancer.

Brian Vest, a professor in computer science at the University of Copenhagen,realised that the lightning fast processor in Playstation 3 can double as ahome computer. Together with specialists at the Bioinformation Research Centreat Aarhus University, he developed a method for applying the gaming machine'sprocessor to help crunch data about prostate cancer.
'The machine is ten times faster than a normal computer so by using its enormouscalculating powers we can lighten our work considerably,' Vest told Nyhedsavisennewspaper.

Playstation owners involved in the project simply install a program, link theirconsole to the scientists' network via the internet and then let the machine dothe work. While the owners rest their hands and fingers for the next round ofArmored Core, the machine searches a DNA chip that contains genetic materialfrom 2000 people. The goal is to locate the gene that causes prostate cancer.

Some 100 Playstation owners have participated in the project since January.

Dr Jørgen Kvist Kristensen at State Hospital's Urology Department is hopeful theproject can give insight into who develops prostate cancer, which is the secondmost fatal form of cancer among Danish men.

'That would give us the possibility to manipulate the disease so it neverdevelops,' Kristensen said.

Stub from http://www.cphpost.dk/get/101009.html

Biophysics

Biophysics (also biological physics) is an interdisciplinary science that applies the theories and methods of physics, to questions of biology. Biophysics research today comprises a number of specific biological studies, which do not share a unique identifying factor, nor subject themselves to clear and concise definitions. The studies included under the umbrella of biophysics range from sequence analysis to neural networks. In the recent past, biophysics included creating mechanical limbs and nanomachines to regulate biological functions. Today, these are more commonly referred to as belonging to the fields of bioengineering and nanotechnology respectively.

> read full article at Wikipedia.org

Best of Bioinformatics' Book: Hand Picked

Hi 2 all,

I recently browsed through the available books, magazines for bioinformatics for the convenience of my blog readers . I hand picked some books that all bioinformaticists must need that u may not aware of.. So u can find the books that i've picked in the following page..

BIOINFLUX STORE

Language created for describing genes

source: ScienceDaily

A U.S.-led international group of scientists has expanded a lingua franca used to describe the activities of genes in living organisms.

The expansion is part of the unified language called Gene Ontology, which provides terms that scientists can use to describe the complex events that occur when a pathogenic or beneficial microbe encounters its host.

The initiative is part of the Plant-Associated Microbe Gene Ontology project, a recently-established interest group of the worldwide Gene Ontology Consortium, supported in part by the U.S. National Science Foundation.

Professor Brett Tyler of the Virginia Bioinformatics Institute, located at Virginia Tech, said, "By providing a precise vocabulary for the functions of these genes, scientists can compare among microbes the many processes that make up the interplay between a microbe and its host."
The PAMGO consortium is a collaboration of the Virginia Bioinformatics Institute, Cornell University, North Carolina State University, the University of Wisconsin-Madison, The Institute of Genomic Research and Wells College.

Molecular Biology : The molecular post office inside the cell

For most proteins, there is a particular place inside a cell where they carry out their function. But how do they get there? Scientists from the Charité Berlin, the University of Heidelberg, and the Max Planck Institute for Molecular Genetics in Berlin have now been able to visualize the structure of a "molecular machine" involved in protein sorting using cryo-electron microscopy and single particle analysis. This "machine" is made up of a single active ribosome, plus a special signal recognition protein and a matching receptor. The scientists have shown that when the three proteins interact, certain areas open up on the ribosome, which allows the ribosome to dock onto another complex. The later complex, which is called translocon complex, takes over the job of transferring a newly produced protein through the membrane. Knowing the structure of the molecular machine helps scientists to understand how secretory and membrane proteins in a cell are expressed and sorted (Science, May 5, 2006).

Sorting proteins is fundamental to the gene expression of every organism - from bacteria to humans. Particularly important during biosynthesis is sorting secretory and membrane proteins, which have to find the way to their final destination inside or outside the cell. Secretory proteins are those that later on leave the cell, like anti-bodies. Membrane proteins are proteins embedded into the cell's membranes - for example, signalling receptors. One particular molecular complex is important in protein sorting. It is made from an active ribosome - that is, the protein synthesis machine in the cell - called the signal recognition particle (SRP), and its corresponding receptor. It is the structure of this complex that the scientific team is now able to describe.

The key element to this machine's functioning is a signal sequence located at the N-terminal end of the protein to be sorted. The sequence acts as a kind of "postal code" in the cell. The SRP reads the sequence as soon as the newly built protein chain leaves the ribosome. The SRP binds to the ribosome and directs it, together with the SRP receptor, to what is called the "translocon complex" in the membrane of the endoplasmic reticulum. The translocon complex is made of a "protein conducting channel" and other membrane proteins. The ribosome is anchored at the translocon and continues with protein biosynthesis.Notable is that the ribosome can no longer bind to the translocon as soon as the SRP has bound to the ribosome. The ribosome needs additional support from the SRP receptor, which it transfers from the SRP to the translocon. Now that scientists understand the structure of the complex, they can see how the receptor interacts with ribosome and SRP and replaces parts of the SRP molecule. In this way, specific sites are made available for the translocon, which allows it to bind to the ribosome. Understanding this key event during protein sorting is essential to understanding how secretory and membrane proteins are expressed in a cell.

--http://www.mpg.de

Sorry! No updates!!

Hi to all my BLOG subscribers,

Sorry, i cudn't post blog posts 4 the recent time due 2 server running low on fuel in our research lab.. But anyway, am still striving hard 2 put forward the information watever i get.. Thanks 2 one and all 4 regularly turning 2 my blog...

Various Structure Prediction Methods

Structure Prediction in 1D

• Limited computing resources and experimental inaccurices prevent prediction of protein structure from first principles. Therefore, the only succesful structure prediction tools are knowledge-based, using a combination of statistical theory and empirical rules.
  

Secondary Structure Prediction Methods

• Basic concept: segments of consecutive residues have preferences for certain secondary structure states: a pattern recognition problem (helix, strand or coil or loop). Physicochemical principles, rule-based devices, expert systems, graph theory, linear and multilinear statistics, nearest-neighbor algorithms, molecular dynamics, neural networks. The main limitation is the use of only local information, which is estimated to play for roughly 65% of secondary structure formation. To improve predictions, it is key the use of evolutionary information.
  

•  Programs: PHD, JPred2 (JNet, NSSP, PREDATOR, PHD), PSIRED, SSPro2, HMMSTR/I, etc.
  

• Specialized methods: coiled-coil predictions. A coiled coil is a bundle of several helices assuming a side-chain packing geometry ("knob-into-holes"). COILS.
  

Solvent Accesibility Prediction Methods

• Basic concept: try different arrangements and assess them by predicting the extent to which a residue embedded in a protein structure is accesible to the solvent. PDH, PROFphd, JPred2 server.
  

Transmembrane Helix Prediction Methods

• Transmembrane proteins still represent a challenge. They do not crystalize, and are hardly tractable by NMR spectroscopy. Prediction is simplified by the fat of the lipid bilayer of the membrane, which reduced the degrees of freedom making the prediction almost a 2D problem.
  

• Basic concept: TM helices are predominantly apolar and between 12 and 35 residues long, globular regions between membrane helices are typically shorter than 60 residues, most TMH proteins have a specific distribution of the positively charged amino acids Arginine and Lysine (the "positive-inside-rule").
  

• Programs: ToPred2, MEMSAT, TMAP, PHD, TMHMM, HMMTOP
  

Public Servers

PHDsec,PROFsec  : neural-network based prediction of secondary structure, accessibility                                            and TMH.
JPred, Jpred2       : neural networks, evolutionary information. Version 2 evaluates results                                         from 4 different neural networks (JNet, NSSP, Predator, PHD).
PROF                         : multiple alignments and other characteristic from databases.
PSIpred                    : based on profiles created by psi-blast and neural networks.
SAM-T99                  : neural network and HMM.
SCRATCH                 : uses SSPro (recursive bidirectional neural networks).