Showing posts with label drugs. Show all posts
Showing posts with label drugs. Show all posts

Thursday, February 2, 2012

Protein drugs to facilitate easier treatment of cancer

Scientists have discovered a new physical form of proteins that could drastically improve treatments for cancer and other diseases, as well as overcome some of the largest challenges in therapeutics.
The protein formulation strategy, developed by researchers at The University of Texas at Austin, is unprecedented and offers a new and universal approach to drug delivery one that could revolutionize treatment of cancer, arthritis and infectious disease.
“We believe this discovery of a new highly concentrated form of proteins – clusters of individual protein molecules – is a disruptive innovation that could transform how we fight diseases,” Keith P. Johnston, a chemical engineering professor and member of the National Academy Engineering, said.
“It required integration of challenging contributions in fundamental science and engineering from three of our chemical engineering research groups,” he said.
Johnston, Chemical Engineering Professor Thomas M. Truskett and Assistant Professor Jennifer Maynard have led the research.
“The real challenge in developing therapeutics is how do you deliver them to patients,” Maynard said.
Typically, protein biopharmaceuticals are administered intravenously at dilute concentrations in a hospital or clinic. Scientists and engineers have long tried to produce safe drugs at higher concentrations, so that a patient could self-inject the drugs at home, similar to an insulin shot.
However, doing so has been stymied by the fact that proteins, in high-concentration formulations, form aggregates that could be dangerous to patients and gels that cannot be injected.
The Cockrell School research team has introduced a new physical form of proteins, whereby proteins are packed into highly concentrated, nanometer-sized clusters that can pass through a needle into a patient to treat disease.
The novel composition avoids the pitfalls of previous attempts because drug proteins are clustered so densely that they don’t unfold or form dangerous aggregates.
“This general physical concept for forming highly concentrated, yet stable, protein dispersions is a major new direction in protein science,” Johnston said.
A key advance came in 2004, when Truskett predicted that protein-based drugs in solution would be stable if they could somehow be formulated at ultra-high concentrations. At that time, Johnston had nanoparticles of concentrated stable protein but didn’t know how to disperse them in an injectable form.
In 2009, the team formed protein nanoclusters in water simply by properly adjusting the pH (to lower protein charge) and adding sugar to crowd protein molecules together. Upon dilution or subcutaneous injection into a mouse the proteins separate back to individual stable molecules with biological activity.
Once injected, the protein in the bloodstream attacks targeted cells and tumors similarly as for protein delivered via IV therapy. To provide a roadmap for improving the design of nanoclusters, chemical engineering graduate students, Andrea Miller and Ameya Borwankar worked with Truskett and Johnston to develop a new thermodynamic theory.
Another breakthrough for the team came in 2009 when a chemical engineering senior, Brian Wilson, created a transparent dispersion of extremely concentrated protein, which was later found to be formed of nanoclusters.
The study has been published online in the ACS Nano journal.

Tuesday, August 24, 2010

Roche Enters $1.1B Drug Deal With US's Aileron Therapeutics for New Stapled Peptide Therapeutics

Aileron Therapeutics and Roche announced today that they have entered into a collaboration to discover, develop and commercialise a new class of drugs called Stapled Peptide Therapeutics. As part of this agreement, Roche will work with Aileron to develop drug candidates against up to five undisclosed targets selected from Roche’s key therapeutic areas, which include oncology, virology, inflammation, metabolism and CNS.


Stapled Peptide Therapeutics are a result of Aileron’s breakthrough peptide stabilization technology, and are a potential solution to drug as-yet intractable disease targets, including those originating from long sought-after intracellular protein-protein interactions.


Under the terms of the agreement, Roche will provide Aileron guaranteed funding of at least $25 million in technology access fees and R&D support. Aileron is eligible to receive up to $1.1 billion in payments upon the achievement of discovery, development, regulatory and commercialisation milestones, if drug candidates are developed against all five targets. In addition, Aileron will receive royalties on future sales for any marketed products that result from the collaboration. Aileron will have substantial responsibility in collaboration with Roche to develop drug candidates against the selected targets up to clinical development.


Do you want to know more?


Share |

Tuesday, June 1, 2010

Search PubMed with the advanced Semantically Annotated Biomedical Search XTractor Lite


Try it! on your websites & Blogs

Sandoz to Acquire Oriel Therapeutics

Sandoz has signed a definitive agreement to acquire Oriel Therapeutics, a privately held US pharmaceuticals company, gaining exclusive rights to a portfolio of generic drug candidates and related technologies targeting medicines in the inhalable respiratory drug market. Terms of the deal were not disclosed.



The latter focuses on developing respiratory products with known pathways as generic alternatives to patented drugs for asthma and chronic obstructive pulmonary disease (COPD).



The acquisition provides the former with three development projects targeting leading medicines in this field. Regulatory approvals of these medicines, if achieved, would enable the former to increase access to affordable, quality therapeutic alternatives for these increasingly prevalent diseases. Details of the latter's development programs, including anticipated timing of future regulatory submissions, are not disclosed for competitive reasons.



The acquisition of the latter, which will be integrated as a separate development unit within the former, also offers Sandoz access to FreePath drug delivery technology. This has the potential to address some of the hurdles facing regulatory approval of generic inhaled medicines in the US.

Sandoz to Acquire Oriel Therapeutics

Sandoz has signed a definitive agreement to acquire Oriel Therapeutics, a privately held US pharmaceuticals company, gaining exclusive rights to a portfolio of generic drug candidates and related technologies targeting medicines in the inhalable respiratory drug market. Terms of the deal were not disclosed.


The latter focuses on developing respiratory products with known pathways as generic alternatives to patented drugs for asthma and chronic obstructive pulmonary disease (COPD).


The acquisition provides the former with three development projects targeting leading medicines in this field. Regulatory approvals of these medicines, if achieved, would enable the former to increase access to affordable, quality therapeutic alternatives for these increasingly prevalent diseases. Details of the latter's development programs, including anticipated timing of future regulatory submissions, are not disclosed for competitive reasons.


The acquisition of the latter, which will be integrated as a separate development unit within the former, also offers Sandoz access to FreePath drug delivery technology. This has the potential to address some of the hurdles facing regulatory approval of generic inhaled medicines in the US.

Sunday, May 30, 2010

GSK and Online Communities Create Unique Alliance to Stimulate Open Source Drug Discovery for Malaria

- GSK becomes first company to freely share chemical structures on 13,500 molecules from its compound library
- Alliances formed with leading scientific research communities from private industry and public-domain data provider

courtesy CDD Blog
Logos
GlaxoSmithKline (GSK) had teamed up with leading public-domain data providers European Bioinformatics Institute (EMBL-EBI), the U.S. National Library of Medicine (NLM) and the US-based informatics service provider Collaborative Drug Discovery (CDD) to make freely available key scientific information on more than 13,500 compounds that could ultimately lead to new treatments for malaria.

The release of this data marks the first time that a pharmaceutical company has made available the structures of so many compounds and is made possible through the collaboration of the web hosts and their specialist research tools, which will be available at no cost to researchers. The information, which is hosted on websites regularly used by researchers, includes high quality scientific data about the molecules from GSK’s own compound library which have demonstrated potency against the most deadly malaria parasite, P. falciparum.

“We are delighted that EMBL-EBI, NLM and CDD have joined us in this worthwhile endeavour to apply the principles of open source to drug discovery for malaria,” said Patrick Vallance, head of drug discovery at GSK. “Defeating this disease will require many scientific minds working together. We hope researchers from across the world will now use this information to drive further studies, and that other groups from pharmaceutical industry to academia will add their information to this on-line resource.”

This type of data is the first step on the road to developing new medicines. With the structure of the compounds and information about where they affect the malaria parasite, scientists could then carry out further research on these compounds for drug discovery or to understand how these might be used to inhibit the parasite’s life cycle and ultimately lead to new medicines. Opening up this information widely is essentially an example of ‘open source’ tactic being applied to drug discovery.

“Making life-science information openly available to the research community is at the heart of the EMBL-EBI’s mission,” added John Overington, leader of the EMBL-EBI’s ChEMBL team, which will act as the primary repository for the data through its ChEMBL resource. “We’re proud to be able to add value to the GSK data by incorporating it into ChEMBL and linking it with a vast array of information that could help researchers to find new treatments for malaria. This is the beginning of a new era of public–private collaboration in drug research.”

“NLM is excited to be involved in this groundbreaking release of information to the public,” said Steve Bryant, head of NLM’s PubChem database, which is housing the data. “By making these data available through public resources such as PubChem, GSK is greatly facilitating the research process, as the information is linked to related compounds, bioactivity results, published literature, and other resources that will assist researchers in making new discoveries to combat malaria.”

“CDD is delighted to be playing a role in this truly historic event,” commented Barry A. Bunin, CEO of Collaborative Drug Discovery. “In decades of medical breakthroughs from Big Pharmas, this is the first time a group is openly sharing all the chemical and biological data – not just the few hits. Furthermore, for phenotypic screens, the CDD tools allow researchers to begin to hypothesize and validate the targets from the whole cell screens.”

EMBL-EBI will act as the primary repository for the data on this compound set, and will index and format further information that is contributed. GSK will add more information as it is generated and external scientists researching these compounds and the data will be asked do the same.

About the data

The data contains the ‘hits’ or results from a screening of the 2 million compounds in GSK’s compound library to determine the effect of these compounds on the malaria parasite. The screening project identified ~13,500 compounds that showed strong inhibition on the parasite.

Kinase inhibitors constituted a large proportion of the molecules with previously known activity and now identified as antimalarial hits. The data includes the chemical families that GSK is currently researching for this indication and the ‘mechanisms of action’ for those compounds which the company has previously tested for other indications.

Most of the compound structures identified have been classified as capable of being converted into medicine.

The current microbiological information for the compounds and the structures have been put on online resources that are easily accessed by researchers. The EMBL-EBI site has been constructed so that scientists globally can add their data to the information there, with access free to all. The value of the release of information is enhanced by the collaboration of the web hosts and the specialist research tools on the site, that are being made available to researchers at no cost to them.

GSK gratefully recognises the support of Medicines for Malaria Venture, which contributed funding for this project.

Full information can be viewed online at:

www.ebi.ac.uk/chembl/

http://pubchem.ncbi.nlm.nih.gov/

www.collaborativedrug.com/

Do you want to know more?

Sunday, January 24, 2010

Transfer of pharmaceutical data resources, private to public domain has greatest impact

While this is very encouraging what's going to be it's impact on the industry on proprietary database vendors? More & more of open database consortia and open curation models are on the offing, with high level of participation from both the academia and the Industry.

The European Molecular Biology Laboratory's European Bioinformatics Institute has launched a "vast online database" of genomic-based drug and small molecule information available in an open access format for researchers seeking new therapeutics, according to EMBL-EBI.

The ChEMBLdb holds translational information on more than 520,000 small molecules, including data on target binding, the affect these compounds have on cells and organisms, and information about the molecules' absorption, distribution, metabolism, excretion, and toxicity.

"The data lie at the heart of translating information from the human genome into successful new drugs in the clinic," EMBL-EBI said this week.

EMBL-EBI is hosting the database, which was transferred from the biotech company Galapagos through a £4.7 million ($7.7 million) Strategic Award from the Wellcome Trust.

"This unprecedented transfer of pharmaceutical data resources from the private sector to the public domain should have the greatest impact on researchers in academia and in small companies on limited budgets," Alan Schafer, director of science funding at the Wellcome Trust, said in a statement.

"ChEMBLdb will be a major resource of information for driving forward medicinal chemistry and drug development in the UK and internationally," Schafer said.

EMBL-EBI also said that, along with partner Wellcome Trust, it has released an integrated resource of sequence, compound, and screening data from a range of sources for protein kinases, called Kinase SARfari.

Tuesday, December 15, 2009

GlaxoSmithKline to Buy Stake in Intercell AG

GlaxoSmithKline Plc will buy a stake in Austria’s Intercell AG in a move that analysts said underscores drugmakers’ growing interest in vaccines. Glaxo will pay 33.6 million euros ($49.5 million) as part of the alliance to develop and market Intercell’s needle-free, patch-based immunizations for traveler’s diarrhea and pandemic influenza. The London-based drugmaker also will buy as much as 5 percent of Intercell for up to 84 million euros via a staggered shareholding option, the companies said in a statement today.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.









Thursday, December 10, 2009

World's fastest growing Semantic discovery & Expert Curated Knowledgebase platform crosses 500,000 biomedical facts now

Indian Life Sciences Informatics Company, Molecular Connections announced today, that their XTractor Premium platform now has more that 503,985 "Expert" annotated biomedical facts from literature and is the fastest growing knowledgebase currently.

XTractor Premium platform is Fast Becoming the definitive Semantic Knowledge discovery & Expert curated Knowledgebase for Life Science Researchers. The XTractor Premium Knowledgebase in addition to more than 503,985 relationships on proteins, drugs, biological process and diseases has advanced semantic search, concept linking analytics for effective knowledge discovery and modeling.

XTractor Premium provides Precision based mining of the most relevant facts. Compared to natural language processing engines, manual annotation approach reduces false positives rate by 12-35%.

XTractor premium serves as a platform to stay current with weekly updates from PubMed. Provides “Topic Tracking” with email alerts on specific biological entities of interest via the “Watch List” feature.

The Highlights

Semantic Search: The first of its kind highly advanced search feature, where in one could query the XTractor Premium Knowledgebase using multiple ontologies. This would enable you to narrow down on your targets at ease.

Concept Linking: Our advanced query feature would enable you to make assumptions from multiple abstracts, and discover facts, which are hitherto not published.

Bibliographic search: Search based on author, organization, affiliation or country.

Save Export and Visualize: Save and export the data in user-friendly formats, also XTractor Premium is made compatible with CytoScape - so one can visualize the networks rendered using a in-house CytoScape plug-in.

Web based and onsite installation available

To know more about the advantages of the XTractor Premium and to register for a free trial account and a webex demo please visit XTractor Premium portal www.xtractor.in/premium.

About XTractor Premium Knowledgebase
XTractor knowledgebase currently contains 503,985 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions, toxicity, pharmacokinetics, disease mechanisms. It is the Only Knowledgebase that gets updated everyday with manually annotated relationships from the latest PubMed publications and contains more than more than 1,269 Unique Drugs, 3,602 Unique Diseases, 11,407 Unique Proteins, and 3,266 Unique Biological Processes. Hence in no time one gets to access one of the largest and the most current manually annotated datasets across the world.

About Molecular Connections
Molecular Connections is a pioneering In silico Discovery Services Company. It provides high quality, cost effective curation, literature informatics solutions and annotation services as well as products. Dr. Limsoon Wong is the Chairman of Molecular Connections. Customers of Molecular Connections include leading pharmaceutical and biotechnology, drug discovery, genomics, proteomics, medical technology, equipment companies and academic institutions spanning across the globe. In addition, Molecular Connections has powerful tool development, database integration, effective data visualization capabilities, specific expertise in building knowledge bases for rapidly growing needs in, ADME Tox, clinical, drugs, chemistry and patent industries. For more information write to us at xtractorpremium@molecularconnections.com

Recent Awards
Deloitte Technology Fast 50 India Winners |Deloitte Technology Fast 500 APAC Winners |CNBC - ICICI Emerging India Awards ‘Small Enterprise of the Year’



XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.









Wednesday, October 14, 2009

Entrez Gene outlink Integration for XTractor

Entrez gene is the most widely used data resource for Gene based information worldwide. To enable researchers to obtain high quality manually annotated information from XTractor when they search for a Gene on Entrez Gene, we are now providing direct links from Entrez Gene records to corresponding Gene Reports in XTractor.

To use this outlinked option- when in Entrez Gene, for any human gene select the “Link Out” option from the Display menu in Entrez Gene and click on the XTractor link. You will be taken directly to the XTractor graphical report for the Gene of interest and also manually annotated facts on the associated Diseases, Drugs and the Biological Processes for the Gene.

Entrez Outlink
http://www.xtractor.in/ncbiSearch.do?xid=XT_15377&symbol=BRCA1



XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.









Wednesday, September 2, 2009

"Achilles' heel of a sizable share of melanomas" - Mutations That May Improve Skin Cancer Treatmen

Mutations in the protein tyrosine kinase gene ERBB4 contribute to — and may provide hints about treating — a subset of melanoma, according to a paper by researchers from the National Institutes of Health and Johns Hopkins University that appeared in the advanced, online edition of Nature Genetics this week.

The team sequenced protein tyrosine kinase or PTK genes in 29 individuals with melanoma. Their search uncovered dozens of somatic mutations affecting the kinase domain of 19 different PTK genes. When they looked at the same 19 genes in another 79 melanoma patients, the researchers found that almost a fifth of those tested harbored mutations in ERBB4.

And, they reported, knocking down the mutated form of ERBB4 or using a drug that targeted the gene slowed the growth of melanoma cell lines, suggesting it might be useful to evaluate ERBB4 status in melanoma patients.

Researchers at the NIH Intramural Sequencing Center sequenced all 86 PTK family genes in tumor samples from 29 individuals with melanoma, picking out somatic mutations by comparing the tumor with matched normal tissue.

Overall, the team detected 30 somatic mutations affecting 19 different PTK genes. When the team sequenced the coding regions of these 19 genes in another 79 melanoma patients, they found 99 non-synonymous mutations.

In particular, 19 percent of the individuals had mutations affecting ERBB4 (also known as HER4), while ten percent carried PTK2B or FLT3 mutations.

Of these, the ERBB4 appeared to be the most severely mutated. As such, the team decided to investigate whether mutations in that gene influenced melanoma growth and/or treatment response, focusing on seven different missense mutations in ERBB4.

The researchers found that the growth of melanoma cell lines containing ERBB4 mutations was curbed when they knocked down the mutated form of the gene using small interfering RNA.

The team was also able to slow the growth of the melanoma cell lines by treating them with the ERBB4-inhibiting drug lapatinib, sold as Tykerb by GlaxoSmithKline.

"We have found what appears to be an Achilles' heel of a sizable share of melanomas," senior author Yardena Samuels, a researcher with the National Human Genome Research Institute's Cancer Genetics Branch, said in a statement.

The team plans to do a clinical trial looking at whether lapatinib is effective for treating melanoma in patients who carry ERBB4 mutations. Steven Rosenberg, chief of surgery at the National Cancer Institute and a researcher with the NIH's clinical center will reportedly head the trial.

"We envision a day when each cancer patient will have therapies tailored to the specific genetic profile of his or her tumor," NHGRI Director Eric Green, said in a statement. "Ultimately, this should lead to more effective and less toxic approaches to cancer care." Green was not directly involved in the current study, but heads the NIH sequencing center that generated the sequence data.



XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.









Saturday, August 8, 2009

Search Wars Episode II. Yebol a new search!

One of my recent post discussed the dawn of the new era and new breed of search engines Search Wars.

YEBOL
a youngling from the the Stanford stable, a new search in the block.
Yebol's mission is to build human-like world's knowledge base and provide knowledge based search (semantics) and services.

Yebol utilizes a combination of patented algorithms paired with human knowledge to build a Web directory for each query and each user. Instead of the common “listing” of Web search queries, Yebol automatically clusters and categorizes search terms, Web sites, pages and contents.

Yebol allows for a multi-dimensional search result instead of the normal one-dimensional search seen by most web search engines today. This provides a more accurate summary of top sites and categories; a wider array of related search terms; a longer and richer expansion for query results; and a deeper base of links and keywords in search result pages.

Unlike current search platforms, Yebol provides hundreds of easily identified and accessibly categorized results in one easily navigable page. The results not only provide users with a rich search experience, but also help them quickly scan the results to find targeted information. In essence, generate a unique “homepage look” for each search query.

Yebol provides a productive experience for both main types of search – general investigation of a topic and specific target search. For users who want to research and explore a topic, Yebol provides rich information from several dimensions. For users who want a specific type of targeted results, they can quickly focus on their category and navigate to the target.

A search for APOE, top most hit (first) gave a expanded definition Apolipoprotein E - on Wikipedia. Followed by link to GHR, wikigenes, gene cards, AD genetics fact sheet form NIA.

It also gives live context sensitive Twitter streaming too.

XTractor Premium - A Platform for discovery, knowledge sharing, analysis and modelling of published biomedical facts.









Thursday, August 6, 2009

BioFocus, Oncodesign Strike Partnership

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.









Friday, June 12, 2009

Search Wars

A not very long time ago, in a galaxy near,
very near by....
SEARCH
WARS
Search, Search engines, While the Search engine big wigs fight for a niche in the search engines landscape .... The Google, Yahoo & now Micorsoft too (with their Bing)

There are the Wolfram|Alpha likes that are forming a separatist and slowly gaining power over the Google order. In fact google has managed to bring balance to both with its Google Squared.

While platforms like XTractor, NextBio, Novoseek, GoPubMed, BioMedSearch have specialized in searching biomedical and biological knowledge are even more strengthening the separatists.

Now to see and know who is more powerful, the galactic empire or the separatist? I leave it to the 'Republic' i.e. You users! to judge, in the form of your comments and experiences with such tools and searches! you could even voice your opinions here









Wednesday, May 6, 2009

XTractor Premium for scientists to access data stored in PubMed says Knowledgespeak

Life sciences informatics company Molecular Connections, India, has announced the availability of XTractor Premium, a knowledge management platform, for the biomedical research community. The product is projected to provide scientists with new and refined ways to access the latest scientific facts from PubMed. Pharmaceutical companies, researchers and scientists can use the platform to identify, verify and develop predictive relationships from PubMed Literature.

Leveraging the ability to transform data to knowledge and to assist experts is seen to be crucial to the success of research investigation today. XTractor Premium offers several enhancements over the beta version in managing large volume of published biomedical data to accelerate decision making.

The XTractor knowledgebase currently contains 150,000 relationships on biomarkers, clinical trials, pathways, knockout studies, mutations, drug interactions and disease mechanisms. The knowledgebase is updated everyday with manually annotated relationships from the latest PUBMED publications. Other premium features include semantic search functionality; concept linking; bibliographic search; and the option to save and export data in user-friendly formats.

Click here







Tuesday, May 5, 2009

The XTractor Premium Knowledgebase surpasses 150000 mark

XTractor Premium - a platform for discovery, analysis and modelling of published biomedical facts. The application also comes with -XTractor Premium Knowledgebase - the only knowledgebase, which provides "manually" annotated facts from PubMed on a daily basis.The XTractor Premium Knowledgebase now has more than 150000 relationships.

TAGS: text mining, manual annotation, data alerts, pubmed, genes, drugs,
processes, diseases, free, data mining, tag, drug discovery, web 2.0,
natural language processing, data analysis, visualization, concept
linking, abstraction, precision, recall, data accuracy, proteins,
interactions, index, query, MeSH, NLM, manual curation, protein
interactions, abstraction, abstracts, accuracy, accurate, data,
annotations, biological process, biomedical literature, categorization,
colloborations, concept linking, curate, curation, data accuracy, data
alerts, literature, categorization, colloborations, concept linking
curate curation data accuracy data alerts da, abstracts, annotations,
biological process, categorization, colloborations, data accuracy, data
analysis, data mining, drug discovery, MeSH, molecules, natural
language processing, NLM, NLP, precision, processes, protein function,
protein interactions, publishing, pubmed, query, recall, tag, text
gathering, visualization, web 2.0

XTractor Premium - A Platform for discovery, analysis and modelling of published biomedical facts.









Wednesday, April 22, 2009

Tracking common gene polymorphisms across multiple Diseases with XTractor Premium


text mining, manual annotation, data alerts, pubmed, genes, drugs, processes, diseases, free, data mining, tag, drug discovery, web 2.0, natural language processing, data analysis, visualization, concept linking, abstraction, precision, recall, data accuracy, proteins, interactions, index, query, MeSH, NLM, manual curation, protein interactions, abstraction, abstracts, accuracy, accurate, data, annotations, biological process, biomedical literature, categorization, colloborations, concept linking, curate, curation, data accuracy, data alerts, literature, categorization, colloborations, concept linking curate curation data accuracy data alerts da, abstracts, annotations, biological process, categorization, colloborations, data accuracy, data analysis, data mining, drug discovery, MeSH, molecules, natural language processing, NLM, NLP, precision, processes, protein function, protein interactions, publishing, pubmed, query, recall, tag, text gathering, visualization, web 2.0


XTractor Premium - A Platform for discovery, analysis and modelling of published biomedical facts.









Tuesday, March 31, 2009

Indian researchers find the pathway to cancer

BANGALORE, Indian Researchers have achieved a breakthrough, identifying a protein pathway that triggers cancer in the human body owing to its erratic behaviour.

Researchers at Bangalore’s National Centre for Biological Sciences (NCBS) led by Satyajit Mayor and Neha Vyas have identified what is known as the Hedgehog pathway and the ways in which it forms and leads to cancer. The researchers, who have published their work in the journal, Cell, say this pathway is formed when the proteins (called hedgehog), which are separate, get drawn to each other by electrostatic interactions between amino acids present around the proteins.

A small cluster of proteins then gets formed and goes on to form a mega-cluster. This travels to other cells and creates effects that are good or bad — the cluster could be normal and help organ regeneration or tissue repair, or the cluster could get hyperactive and affect other cells, which is the sign that cancer is coming.

Simply put, the NCBS research indicates that hyperactivity of the hedgehog proteins within the human body can cause cancer and that its cluster formation has to be prevented to eliminate the possibility of hyperactivity entirely.

“Identifying the initial step that initiates the electrostatic attraction between amino acids that bring together hedgehog proteins in a cluster might help other scientists to design an anti-cancer drug that could stall a mutant hedgehog pathway in effective ways,” Said Neha. Such a drug could target the very source of these attractions — the amino acids that cause them — which are the first cause of cancer.

XTractor Premium - A Platform for discovery, analysis and modelling of published biomedical facts.









Friday, March 20, 2009

Pioneering Biomedical Web Community Poised For Leap To Web 3.0

The Alzheimer Research Forum (http://www.alzforum.org), a dynamic, biomedical Web community that is heavily used by Alzheimer researchers around the world, is preparing to migrate to a new platform that will enable it to more fully exploit social networking ("Web 2.0") and the Semantic Web ("Web 3.0"). Founded 13 years ago when the Web was still in its infancy, the "Alzforum" has more than 5,000 registered members and is familiar to most Alzheimer scientists in the world.

Ever since launching in 1996, the Alzforum Web site has been interactive, posting researchers' comments on published papers and research news. The site has published thousands of peer commentaries and mini-reviews by leading scientists in the field, and has established itself as the "go to" Web site for anyone who wished to be up to date on Alzheimer research. Members can post commentaries on any journal article or news story, and can participate in live discussion forums. Researchers frequently reference Alzforum in scientific papers and conduct weekly "Alzforum" sessions in their labs to discuss current findings. The AlzGene database, designed and curated by researchers at Massachusetts General Hospital and developed and hosted by Alzforum, is a workhorse of the global genetic community, and has generated a primary research publication in Nature Genetics. Alzforum has built numerous other data resources for the research community.

This spring, Alzforum will re-develop its site using the Scientific Collaboration Framework (SCF), a project based on open-source Drupal technology that is designed for building scientific Web communities. SCF was piloted by the Harvard Stem Cell Institute to build a Web publication called StemBook (www.stembook.org). Alzforum will develop some new software modules in Drupal and contribute them back to the SCF, where they will be freely available for other research organizations that are building their own Web communities. (SCF software is available at http://www.sciencecollaboration.org).

SCF is well-suited for publishing articles, comments, forums and blogs, and for managing member communities with fine degrees of editorial control. "We want it to be very easy for anyone to participate, but it's also essential for our editors to vet all postings in order to maintain civil and productive discourse," says Alzforum's co-founder and Executive Editor June Kinoshita.

A feature of SCF that Alzforum's editors are excited about is a semantic tagging module that locates scientific terms within an article, such as names of genes, organisms, and biological processes, and proposes them as tags that describe key concepts in the article. The tags enable the user to search other content with matching or related tags, so that an article about a gene can be automatically linked to a description of the gene, to articles about the gene, and even to the profiles of scientists who study that gene.

"The possibilities this opens up for scientists to navigate a knowledge network of articles, databases, and people is amazing," says Kinoshita. "And all of the Web communities that share the SCF platform will be interconnected. Alzforum has always been about building a research community without walls. Using the SCF, we will take this idea to a whole other level."













Monday, March 16, 2009

Molecular Connections Launches XTractor Premium for Effective Knowledge Management and real time access to Biomedical data

Bangalore, India — Indian Life Sciences Informatics Company, Molecular Connections announced today, the launch of XTractor Premium (www.xtractor.in/premium), a new Knowledge Management Platform designed to enable Pharmaceutical Companies, Researchers, Scientists identify, verify and develop predictive relationships from PubMed Literature.

“The release of XTractor Premium reflects the evolution of our client’s knowledge management needs and our continued commitment to provide knowledge solutions which add value & bring better efficiencies in Drug discovery,” said Jignesh Bhate CEO Molecular Connections.

Leveraging the ability to transform DATA to KNOWLEDGE to assist experts is crucial to the success of drug development today. XTractor Premium offers several enhancements over the beta version in managing large volume of published biomedical data to accelerate decision making in drug discovery.

Data Search: One would be able to perform searches over the entire XTractor knowledgebase of 120600 relationships on proteins, drugs, biological process and diseases (which is ever growing). On an average more than 600 manually annotated facts get added to XTractor everyday, thus it is the ONLY Knowledgebase that gets updated everyday with manually annotated relationships from the latest PUBMED publications. 733 Unique Drugs, 2254 Unique Diseases, 7626 Unique Proteins, 1449 Unique Biological Processes. Hence in no time one gets to access one of the largest and the most current manually annotated datasets across the world.

Semantic Search Features: The first of its kind highly advanced search feature, where in one could query the XTractor Knowledgebase using multiple ontologies. This would enable one to narrow down on the targets at ease.

Concept Linking: Construct hypothesis from multiple abstracts and discover new facts and relationships, which are hitherto not easily decipherable.

Bibliographic search: Would also enable one to search based on author, organization or country.

Save, Export and Visualize: Provides the utility to save and export data in user-friendly formats. Integration with CytoScape provides better knowledge representation and visualization.

All these Premium Features are available via four licensing options; Academic, Commercial, Governmental and Onsite Installation. XTractor Premium is now available with an Attractive Introductory Offer for Academic Researchers. Subscribe now and save! Visit www.xtractor.in/premium for more details.

Currently, XTractor’s user base includes Abbott, AstraZeneca, Bayerhealthcare, Celera, Cephalon, GSK, JNJ, Novartis, Pfizer, P&G, Wyeth, Vertex, USFDA, NIH, NCI, MD Anderson, Harvard Medical School, Max Planck, Scripps Inst. and many more.

About XTractor Premium

XTractor Premium, a platform for discovery, analysis and modeling of published biomedical facts. The application also comes with XTractor Premium Knowledgebase, the only knowledgebase, which provides "manually" annotated facts from PubMed on a weekly basis.

To know more about the advantages of the XTractor Premium and to register for a free trial account and a webex demo please visit XTractor Premium portal www.xtractor.in/premium.

About Molecular Connections

Molecular Connections is a pioneering In silico Discovery Services Company. It provides high quality, cost effective curation, literature informatics solutions and annotation services as well as products. Dr. Limsoon Wong is the Chairman of Molecular Connections. Customers of Molecular Connections include leading pharmaceutical and biotechnology, drug discovery, genomics, proteomics, medical technology, equipment companies and academic institutions spanning across the globe. In addition, Molecular Connections has powerful tool development, database integration, effective data visualization capabilities, specific expertise in building knowledge bases for rapidly growing needs in, ADME Tox, clinical, drugs, chemistry and patent industries. For more information write to us at xtractorpremium@molecularconnections.comThis e-mail address is being protected from spam bots, you need JavaScript enabled to view it

Recent Awards

Deloitte Technology Fast 50 India Winners |Deloitte Technology Fast 500 APEC Winners |CNBC - ICICI Emerging India Awards ‘Small Enterprise of the Year’