Tuesday, June 30, 2009
Sponsored by Indo-US Science & Technology Forum, IISc, JNCASR, DBT, DST, BRNS and CSIR
2nd – 6th July
Jointly Organised by
IISc and JNCASR
Friday, June 26, 2009
LitInspector is a literature search tool providing gene and signal transduction pathway mining within NCBI's PubMed database. The automatic gene recognition and color coding increases the readability of abstracts and significantly speeds up literature research. A main challenge in gene recognition is the resolution of homonyms and rejection of identical abbreviations used in a ‘non-gene’ context. LitInspector uses automatically generated and manually refined filtering lists for this purpose. The quality of the LitInspector results was assessed with a published dataset of 181 PubMed sentences. LitInspector achieved a precision of 96.8%, a recall of 86.6% and an F-measure of 91.4%. To further demonstrate the homonym resolution qualities, LitInspector was compared to three other literature search tools using some challenging examples. The homonym MIZ-1 (gene IDs 7709 and 9063) was correctly resolved in 87% of the abstracts by LitInspector, whereas the other tools achieved recognition rates between 35% and 67%. The LitInspector signal transduction pathway mining is based on a manually curated database of pathway names (e.g. wingless type), pathway components (e.g. WNT1, FZD1), and general pathway keywords (e.g. signaling cascade). The performance was checked for 10 randomly selected genes. Eighty-two per cent of the 38 predicted pathway associations were correct. LitInspector is freely available at http://www.litinspector.org/.
Nucleic Acids Res. 2009 May 5
LitInspector: literature and signal transduction pathway mining in PubMed abstracts.
Frisch M, Klocke B, Haltmeier M, Frech K.
Genomatix Software, 80335 Munich, Germany.
Thursday, June 25, 2009
Monday, June 22, 2009
* P I C
* Cascade PSI-BLAST and
* NS Labpage
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PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been widely used (>1,250 citations in ISI Web of Science), due to its simplicity and a fair accuracy/speed compromise. In the mean time research around PhyML has continued. We designed an efficient algorithm to search the tree space using Subtree Pruning and Regrafting (SPR) topological moves (Hordijk and Gascuel 2005), and proposed a fast branch test based on an approximate likelihood ratio test (Anisimova and Gascuel 2006). However, these novelties were not included in the official version of PhyML, and we found that improvements were still needed in order to make them effective in some practical cases. PhyML 3.0 achieves this task. It implements new algorithms to search the space of tree topologies with user-defined intensity. A non-parametric, Shimodaira-Hasegawa-like branch test is also available. The program provides a number of new evolutionary models and its interface was entirely re-designed. We tested PhyML 3.0 on a large collection of real data sets to ensure that the new version is stable, ready-to-use and still reasonably fast and accurate.
Now available @ /software area !! (NS Group)
WEB SERVER FOR LATEST VERSION PhyML 3.0 Available !!
Friday, June 19, 2009
M.Sc., Bioinfo, Stella Mary's, Chennai.
Proj: Inference on Conformational Variability and flexibility in Proteins Comparison of Crystallographic and Solution Structures.
(Short Term Visitor: worked with Yamunadevi S, NS Group, IISc)
NS Lab Visitor
Heartly wishes in behalf NS Group members..
Sir Richard John Roberts (born September 6, 1943 in Derby) is an English biochemist and molecular biologist. He was awarded the 1993 Nobel Prize in Physiology or Medicine with Phillip Allen Sharp for the discovery of introns in eukaryotic DNA and the mechanism of gene-splicing.
As part of the Platinum Jubilee Celebrations of the Indian Academy of Sciences, a series of Platinum Jubilee Lectures by eminent scientists is being organised to be delivered at different parts of the ountry. In this series a lecture by Dr Richard J. Roberts (Nobel Laureate 1993, New England Biolabs, Beverly, USA) on "Genomics of restriction and modification" will be held at the Faculty all, Indian Institute of Science, Bangalore. on Friday, 19 June 2009 at 4.00 p.m.
More details about Dr. Richard J. Roberts
Thursday, June 18, 2009
TATA INSTITUTE OF FUNDAMENTAL RESEARCH
GKVK, BELLARY ROAD, BANGALORE
Date: Friday, June 19, 2009
Time: 10:15 a.m.
Dr. Arun Krishnan
Lead-Data Mining Group
Monsanto Research Center
Protein Structure Networks: Understanding the organization of protein structures
Ground floor Lecture Hall (LH1)
The architectural organization of protein structures has been the focus of intense research since it can hopefully lead to an understanding of how proteins fold. Despite the difference in models dealing with the way proteins fold into their tertiary structures, it is recognized that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits. However, there are a number of different definitions of what comprises an independent subunit.
In our work, we looked at the organization of protein structures from the smallest unit in sequence space, viz., six-letter "words" to modules that interact with each other in 3D space all the way up to protein domains. We used network representations of proteins wherein the amino acids are the nodes and interactions between them are represented as edges. We identified invariants in protein structures which hold regardless of protein fold or family. Modules identified through our technique were shown through molecular dynamics simulations of the unfolding of ubiquitin to be those that formed early on during the folding process.
Co-ordinator: Prof. R. Sowdhamini (firstname.lastname@example.org)
Monday, June 15, 2009
INDIAN INSTITUTE OF SCIENCE
BANGALORE - 560012
SPEAKER : Ms. Anamika Krishanpal
TITLE : "Genome-wide and structural analyses of protein
DATE AND TIME : Tuesday, 16th June 2009, at 10.30 AM
VENUE : MBU SEMINAR HALL
** ALL ARE CORDIALLY INVITED **
Coffee @ 10:15 AM
12th June ,2009 CHAIRMAN
Sunday, June 14, 2009
Saturday, June 13, 2009
Friday, June 12, 2009
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Monday, June 8, 2009
38221 PDB Entries. 1 Literature Reference. 110800 Domains. (excluding nucleic acids and theoretical models).
IISc SCOP Mirror site