Bio Saga Blog - A Chronicle of Life Sciences & Informatics

              Know About Our Workshop On Bioinformatics and Protein Structure Prediction 10th to 12th May 2019 | Pune, India | 09:30 AM - 05:00 PM Our 3 day comprehensive workshop on Bioinformatics and Protein Structure Prediction aims at providing systematic Hands-on-Training on Protein visualization, mutation & other manipulations.Understand concept of in-silico protein modelling using servers & software’s.Understanding concept of protein motif and domains.Understanding concept of protein structure prediction by Modeller COMPREHENSIVE & SEQUENTIAL SESSIONS ON: ▪ Introduction to Biological databases ▪ Multiple Sequence Alignment – CLUSTALW ▪ Introduction to Proteins & Protein Databases-UNIPROT ▪ Study of proteins and their structures ▪ Protein Secondary Structure Prediction tools ▪ Protein Tertiary Structure Prediction using Servers & Modeller ▪ Protein Structure Validation ...

Is organizing "4 Days Workshop on In silico Drug Discovery (21st-24th Jan2016)” Know about drug discovery & optimize your research work CADD is a rapidly developing branch of chemistry. In the coming days the students who have studied CADD will be required not only in India but  across the globe for advanced research and new discovery.The requirement of trained manpower from the discipline such as Chemistry, Biology and Microbiology is the fuel for the growth of CADD.  Application of CADD is in areas like Agrochemical, pharmaceutical and biotechnological industries, Computational chemistry and library design groups, Chemical software companies, Database developers, Chemical publishers, In-silico Drug Discovery, Toxicity predictions, ADME prediction of Molecules, Chemicals Vendors , R&D, etc. On completion of this workshop you will be expertise in: ü        Analyzing chemical fingerprint ü     ...

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...

The malaria parasite has waged a successful guerrilla war against the human immune system for eons, but a study in this week's Journal of Biological Chemistry has exposed one of the tricks malaria uses to hide from the immune proteins, which may aid in future drug development. Malaria parasites (plasmodia) are transmitted to people via infected mosquitoes. Once inside their human hosts the parasites first set up shop in liver cells, then move into red blood cells (RBCs) to replicate and wait for the next mosquito to help continue the cycle. After plasmodia infect a blood cell, they send out clusters of sticky proteins to the cell surface, enabling them to attach to blood vessels and escape destruction by the host's spleen while they replicate. This tactic can be especially problematic during pregnancy as malaria-infected RBCs congregate in the vessel-rich placenta (the source of food and oxygen for the growing fetus), creating health problems such as anemia, low birth-weight, f...

Here is a abstract that i had submitted at the Plant & Animal Genomes XI Conference January 11-15, 2003 Town & Country Convention Center San Diego, CA. I do not know how relevant is the issue to this day. If any one is interested or if any one is working in these lines, do let me know also pour in your suggestions and comments if any. Fiber quality in cotton is one very vital trait demanding international focus in both scientific and commercial arena. Phytohormones play a major role in all cellular processes in plant development. We have focused our study on the influence of phytohormones in improving the staple length of cotton fiber. There are several pathways, which influence staple length in cotton, among which we have concentrated on the expression pattern of Lipid Transfer Protein3. A cotton fiber protein gene Ltp3, Lipid transfer protein3 (coding for a LTP3 protein), is specifically expressed in fibers at high levels, during the elongation stage. Its levels reach a maxim...

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length. Do you want to know more?

Dr. Ronald Collman talks about exciting new discoveries on HIV, the virus that has taken 25 million lives. Dr. Ronald Collman , professor of medicine in microbiology, virus/cell/molecular core director, Penn Center for AIDS Research, University of Pennsylvania.He describes the molecular structure, pathology, and with great insight, the incredible discoveries that might just help us conquer HIV. Listen to the Original audio source

Here is a abstract that i had submitted at the 3D sig:Structral Bioinformatics at the 1st Structural Bioinformatics Meeting at ISMB 29-30 July 2004, Glasgow, Scotland, UK. I do not know how relevant is the issue to this day. I am interested in working further in this area and i am interested in collaborating. Do let me know your comments also pour your suggestions on how to further this study. In silico methods can be used to design protein, based on stability and functionality using computational methods rather than laboratory procedures (Comet et al., 2000). The changes taking place due to the transfer of motif region from human Catechol-O-methyltansferase to rat Catechol-O-methyltransferase can be studied effectively using computational methods. This will provide insight for further development of the study about the function of neurotransmitter region of catechol-O-methyltransferase and its involvement in the Parkinson’s disease. Catechol-O-methyltransferase (COMT) catalyzes the t...

Many of you involved in structure based drug discovery will know very well about the numerous problems and errors in the data found in the Protein Data Bank (PDB) especially concerning the ligand structures. There have been a lot of publications about such errors, e.g. in Jones et al. J Mol. Biol. (1997) 267 :727, and I heard various conference presentations about this topic too, e.g. by Gerard Kleywegt (University of Uppsala), titled “Protein crystallography: not as simple as ABC then?” at Bryn Mawr, Philadelphia (15-19 October 2007) eChemInfo meeting . The errors are often blamed on the low resolution of the structures involving large protein structures (often thousands of atoms). One would assume that the small molecule crystal structures of the Cambridge Structural Database ( CSD ) do not have such errors, since they have much higher resolution and dealing with small molecules. Let me correct that wrong assumption! Do you want to know more?

By studying the variety of chemical substances and their structures recorded in the CAS REGISTRY SM database, Chemical Abstracts Service (CAS) scientists have discovered that a limited number of molecular shapes are the frameworks for a disproportionately large percentage of reported substances. As shown in the CAS study , half of the known organic chemical substances can be described by just 143 shapes. The analysis, published in The Journal of Organic Chemistry , explains why certain molecular frameworks are more likely to be used in new compounds and may also help identify new regions of chemistry space ripe for exploration.