Bioinformatics Buff!!

I was wondering even when the wet lab results are reported in papers as ‘may be’, ‘possibly’, ‘likely’, which means even wet lab results are not certain. Why then they do keep asking for wet lab “validation” for powerful Bioinformatics works when time and time again, the predictions held true in almost all cases studied?

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Paper again! This time from an International M.Sc student as first author- Second Ever from my Department and School!

(Figure made using PDB ID:5E84)
Paper from an International M.Sc student as first author published in Scientific Reports, Springer Nature Publishing Group! It is entitled “Glucose-regulated protein 78 substrate-binding domain alters its conformation upon EGCG inhibitor binding to nucleotide-binding domain: Molecular dynamics studies”
The link is here:
This is the second paper from an M.Sc student of our Department (perhaps at School level also) and an International one at that.
Congrats to Mr. Sagara and Ms. Aanchal!

Thank you Editor and Reviewers and Scientific Reports team!

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M.Sc project work accepted for publication-First ever from my Department and School!

Wrote this long back. But here goes:

So happy!

My students of 2013-2015 batch have made me proud again.

First ever paper in our Biochemistry Department with M.Sc student publishing as first author! That too, in an International peer-reviewed journal!

The paper entitled “Molecular docking and molecular dynamics studies reveal structural basis and selectivity of inhibitors EGCG and OSU-03012 towards Glucose Regulated Protein-78 (GRP78) overexpressed in Glioblastoma” has been accepted for publication in Journal of Molecular Modeling published by Springer with 2013 IF: 1.863. Here is the link:

Congrats Rituparna and Arpita!

Me musing over setting a benchmark! Paper publishing during M.Sc, making M.Sc dissertation projects to be feasible towards being publication-oriented. And in contributing to raising the scientific temper of the Indian workforce several notches ahead.

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An email I sent: Students do need to be told, even Post-grads

OK Class, we had the class on Data types today. Usually these data types are taken into account but things always have advantages and disadvantages both.
Scientific facts are not absolute facts, they are open to discussion, debate and re-interpretation in context of your experiments.
What you take in all of the different classes Biostatistics, Enzymology, Immunology, Molecular Biology and all, you learn some facts for your solid foundation. Upon these foundations, you build higher up and when you are more capable then do some rational thinking and perform experiments and then re-establish facts. And prove your mentors respectfully wrong. :-).
In fact, this is what learning, discussion and debate is all about. Nothing is perfect in an imperfect world, except the Sun rising and setting and nurturing Life.
So, when you see or observe contradictory lessons, take these in your stride with the attitude that it is for you to grasp the basics and then later build upon it.
So, here is a wikipedia article on Data types with more info:
Enjoy the learning.
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A moment of Glory! And Pride!!

Most read Status of one of my articles on Journal of Biomolecular Structure and Dynamics website:

Accessed: 21 December 2015.

Most Read

Most Read2

Cheers to myself! And to Universe too!! Thanks to everything and everyone.


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After Vacations

Kick-start myself.


Mind? Check! Motivation? Check! Energy? Check! Surroundings? Check! Everything? Check!

Awaiting the new batch of students with renewed vigour. Hope they have the same energy levels,  motivation levels, EQ, IQ and attention and awareness of values like the 2013-2015 batch. Of this batch, on their projectile towards pursuing Doctor of Philosophy, one student will be joining IIT-Bombay, one will be joining Forschungszentrum Jülich – Institute of Complex Systems, Germany, and some others have also been selected to pursue Ph.D. Some of these are still in pursuit, and they appear determined, motivated and inspired to take forward their zeal of pursuing science and Life as well. Cheers and blessings to every single student of 2013-2015 batch.

May the Divine Light shine upon them!

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Ph.D interviews over.

A Ph.D is the highest scholarly achievement in any person’s life. Naturally, a student entering the hallowed portals of a Ph.D life, feels afraid at the first baby steps. Who will I be assigned to? How will my supervisor be? Will I be able to stand on my own and relate and interact empathically with the assigned supervisor? Will life be difficult or easy for me in that place?

Being slightly afraid is all natural. But when you let your fears take precedence over your natural ability to adapt, adjust and living life joyfully, you have not really lived.

Most will take the tried and tested route. Join their own post-graduate supervisors. Easy does it!

Or, if not a post-graduate supervisor, the one whose student went to Germany or US for  a year of work. Even if the poor supervisor is not able to handle all lab Ph.D students going abroad, who cares?

Or the one whose lab is full. Never mind that golden opportunity to learn starting a lab……

Good students, with the ability to think above and beyond the mundane life, are hard to find. This is astonishing,  given the flexibility and intrinsic adaptability of young minds. They are largely resistant to change.


240px-Stephen_Hawking.StarChildStephen Hawking-flashing his million-dollar smile.

Stephen Hawking, among the greatest physicists, despite suffering from a motor neuron disease, has mentored many good doctoral students, notable among them are Raymond Laflamme and Don Page.  As for his own doctoral life, Wikipedia article on him provides some peek and views:

“Hawking’s first year as a doctoral student[2] was difficult. He was initially disappointed to find that he had been assigned Dennis William Sciama, one of the founders of modern cosmology, as a supervisor rather than noted astronomer Fred Hoyle,[139][140] and he found his training in mathematics inadequate for work in general relativity and cosmology.[141] After being diagnosed with motor-neuron disease, Hawking fell into a depression; though his doctors advised that he continue with his studies, he felt there was little point.[142] However, his disease progressed more slowly than doctors had predicted. Although Hawking had difficulty walking unsupported and his speech was almost unintelligible, an initial diagnosis that he had only two years to live proved unfounded. With the encouragement of Sciama, he returned to his work.[143][144] Hawking started developing a reputation for brilliance and brashness when he publicly challenged the work of Fred Hoyle and his student Jayant Narlikar at a lecture in June 1964.[145][146]

When Hawking began his graduate studies, there was much debate in the physics community about the prevailing theories of the creation of the Universe: the Big Bang and the Steady State theories.[147] Inspired by Roger Penrose‘s theorem of a spacetime singularity in the centre of black holes, Hawking applied the same thinking to the entire universe, and during 1965 wrote his thesis on this topic.[148] There were other positive developments: Hawking received a research fellowship at Gonville and Caius College.[78] He obtained his PhD degree in cosmology in March 1966,[149] and his essay entitled “Singularities and the Geometry of Space-Time” shared top honours with one by Penrose to win that year’s prestigious Adams Prize.”

Need I say more?



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