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<!DOCTYPE html>
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<head>
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<meta name="description" content="I define work as what I do for living. As of now, that seems to be research. I work in the field of cheminformatics, which is applying computer science principles to tackle chemical, and biological problems ">
<meta name="author" content="Dipan Ghosh">
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<title>Dipan's Web: Work</title>
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<h1>Current Work</h1>
<figure role="img" class="bannerimage"><img src="./images/Bigdata_Graphics_website.jpg" alt="Cheminformatics Banner Image" class="container"></figure>
<p>Over the years, I have gone to become a tech-nerd of a sort, and that affinity with computers landed me in the BigChem project, for my PhD. The overall idea of this particular project has to do with exploring and utilizing computational methods and strategies to identiy false positives, frequent hitters as we call them, in high throughput assays.</p>
<p>This is a project from the Marie Curie ITN, and that means there would be a whole lot of moving about. Currently I am in Munich, Germany, working with Dr. Igor Tetko in Helmholtz Zentrum München. </p>
</section>
<section class="container">
<h1>Formal Education</h1>
<p>I have been very fortunate to go through one of the best education pipeline in India in my time, and being through that ride has enriched me in a very deep way. From this perspective, I can say, No one can teach anyone, whatever you learn, comes from within. Swami Vivekanada’s words, <q class = "mark">Education is the manifestation of the perfection already in man.</q> Below is a short history of my formal education, and my current CV.</p>
<ul class = "list-unstyled" id="formalEduList">
<li>
<ul class = "list-unstyled">
<li>
<h3 class="course">Secondary</h3>
</li>
<li class="instt">Narendrapur Ramakrishna Mission Vidyalaya</li>
<li class="time">2009 Secondary (Madhyamik)</li>
</ul>
</li>
<li>
<ul class = "list-unstyled">
<li>
<h3 class="course">Senior Secondary</h3>
</li>
<li class="instt">Ramakrishna Mission Vidyapith, Deoghar</li>
<li class="time">2011 Senior Secondary</li>
</ul>
</li>
<li>
<ul class = "list-unstyled">
<li>
<h3 class="course">Bachelor of Science (Research)</h3>
</li>
<li class="instt">Indian Institute of Science</li>
<li class="time">2011-2015</li>
</ul>
</li>
<li>
<ul class = "list-unstyled">
<li>
<h3 class="course">Master of Science</h3>
</li>
<li class="instt">Indian Institute of Science</li>
<li class="time">2015-2016</li>
</ul>
</li>
<li>
<ul class = "list-unstyled">
<li>
<h3 class="course">Philosophy of Doctorate (PhD)</h3>
</li>
<li class="instt">Marie Curie BigChem Fellow.</li>
<li class="time">2017-Now</li>
</ul>
</li>
</ul>
</section>
<article class="container" id="cheminformatics" role="article">
<h1>Demystifying Cheminformatics</h1>
<p>Whenever anyone asks me what do I reaserch on, I am faced with a bit of difficulty. It is not at all easy to express what I do in common language. That is why, I thought it would be good to discuss what I do in a bit of detail here. I also plan to write a blog post about it, I would link it here when I do that</p>
<h3 style="text-align: center">CHEMistry + iNFORMATICS = CHEMINFORMATICS</h3>
<p>Following the etymology, its obvious that it is a hybrid field of Chemistry and informatics. Chemistry is well known but what is informatics? Well, it goes by many names. A quick <a href="https://www.google.com/search?q=define+informatics">google search</a> reveals it means <q>the science of processing data for storage and retrieval; information science.</q>, which might perplex some people even more! In brief it means dealing with computer and data, writing programs and developing algorhythms etc. In cheminformatics we do all this to solve some chemical, or as it often is, biological problems. Let me illustrate with an example</p>
<p>I will pick a problem from core molecular biology, then drift onto drug discovery and chemical biology, finally introducing computation. </p><p>In molecular biology, people often look into various <a href="https://en.wikipedia.org/wiki/Metabolic_pathway" role="link">metabolic pathways</a>, and try to work out how that pathway functions. There are usually a cascade of events, and lots of enzymes are involved, and each separate step needs to be worked out individually, studying one enzyme at a time. Once we get enough picture of a pathway, we can think about ways to influence that by modulating some key partners in the pathway. If that pathway leads to a disease, we might want to block a key enzyme in the pathway. Now the question becomes how do we do that. Over the years, the strategy has been to <q>try something and see what happens</q>, and pretty much all the drug in regular use today in the market were found that way. This is what pharma companies and medicinal chemists are mostly interested in. As systems get more complex, the try and see approach becomes limited in many ways, and one then has to develop a rational of doing this, of finding new compounds, and this area is known as chemical biology. To design, develop, or otherwise find compounds that are biologically relevant. Also, more often than not, compounds needs to be modulated to make the desireable effects potent, or curb out the undesireable effects. This is also chemical biology, that relys upon computation.</p>
<p>However, how do you look for biologically relevant compounds? There are a few ways of attacking this behemoth, and pretty much all of tha relys heavily upon computation. Nowadays, crystal stuctures determined by <a href="https://en.wikipedia.org/wiki/X-ray_crystallography">X-Ray diffraction</a>of many proteins are available, and for many problems, that is the starting point. By determining the structural features of a protein, one can try to design a ligand that would bind that protein, its analogus to trying to come up with a key, by looking at the keyhole. There are serious limitations of this process, due to technical and computational limitations, but this is one method, namely, rational design. The other way, has to do with <a href="https://en.wikipedia.org/wiki/High-throughput_screening">High-throughput screening</a>. This is back to that do and see approach, but here, we try to sample a very large number of compounds, milions of compounds are generally tested. This generated a huge pile of data, that somehow needs to be made sense of, and thats where the computational bit comes in. After you make sense of your screening data, you typically have what are called <q>Leads</q>. These are potential compounds that can become a drug some day. Now, computationally, we can determine its various properties, and see if that compound has any obvious problem, (such as toxicity etc) and try various modifications to see if any one them makes the compound better. By doing this <i>in-silico</i>(in a computer), we can do a whole lot of it very quickly, rather than wasting time and resource making molecules that are of no use. Apart from these, there are computation involved in pretty much every step of the drug discovery pipeline, and that, in brief is what cheminformatics entails.</p>
<p>The project I am associated with is <a href="http://bigchem.eu">BIGCHEM: Big Data in chemistry</a>. This project deals with multiple problems having to do with a large amount of data (like the one I described). If you are interesed, you can find a brief description of all the projects being handled <a href="http://www.lead-discovery.de/wp-content/uploads/2016/02/BIGCHEM_announcement-_3_.pdf">here</a> </p>
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