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My Publications


  1. Molecular Recognition Pattern of Cytotoxic Alkaloid Vinblastine with Multiple Targets. P Pandya, Lokesh Kr. Agarwal, Neelima Gupta, Sourav Pal. (2014), Journal of Molecular Graphics and Modeling Vol 54, Page 1-9 Impact 2.022
  2. Sequence Specific Binding of Beta Carboline Alkaloid Harmalol with Deoxyribonucleotides: Binding Heterogeneity, Conformational, Thermodynamic and Cytotoxic Aspects. S. Sarkar, P. Pandya, K. Bhadra (2014), PLOSOne Vol 9, Page e108022 Impact 3.534. doi: 10.1371/journal.pone.0108022
  3. Thermodynamic Study of Rhodamine 123–Calf Thymus DNA Interaction: Determination of Calorimetric Enthalpy by Optical Melting Study. A. Masum, M. Chakraborty, P. Pandya, U. Halder, Md. Islam, S. Mukhopadhyay (2014), The Journal of Physical Chemistry B, Vol 118, page 13151−13161 Impact 3.377, DoI: 10.1021/jp509326r
  4. Binding of DNA with Rhodamine B: spectroscopic and molecular modeling studies. Md Maidul Islam, Maharudra Chakraborty, Prateek Pandya, Abdulla Al Masum, Neelima Gupta, Subrata Mukhopadhyay. (2013), Dyes and Pigments Vol 99, Page 412-422. Impact 3.468
  5. Structural studies on ligand–DNA systems: A robust approach in drug design. S Kumar, P Pandya, K Pandav, SP Gupta, A Chopra. (2012), Journal of Biosciences Vol 37 (3), Page 553-561. Impact 1.939
  6. DNA Binding Studies of Vinca Alkaloids: Experimental and Computational Evidence. P Pandya, SP Gupta, R Barthwal, B Jayaram, S Kumar. (2012), Natural Products Communication Vol 7, Page 1-5. Impact 0.956
  7. Structural Features of Non-covalent DNA Binding Anticancer Agents. P Pandya, LK Agarwal. 2012, Chemistry News Letter Vol 1, No. 1, Page 67-71. ISBN 2278-6201.
  8. Methylene Linker Assisted DNA Binding of Vinblastine and Simpler Analogs: Purine-Pyrimidine Specificity of Indole Derivatives. SP Gupta, K Pandav P Pandya GS Kumar, R Barthwal S Kumar. (2011), Chemistry and Biology Interface Vol. 1, Issue 2, Page 297-309. 
  9. DNA Minor Groove Binding of Small Molecules: Experimental and Computational Evidence. P Pandya, MM Islam, GS Kumar, B Jayaram & S Kumar. (2010), J. Chemical Sciences Vol. 122, No. 2, March, Pages 247–257. Impact 1.224
  10. RNA targeting through small molecule binding: Studies on t-RNA binding by cytotoxic protoberberine alkaloid coralyne. MM Islam, P Pandya, S Kumar, GS Kumar. (2009), Molecular Biosystems Vol. 5, Pages 244-254. Impact 3.35
  11. Binding of DNA binding alkaloids berberine and palmatine to t-RNA and comparison to ethidium: spectroscopic and molecular modeling studies. MM Islam, P Pandya, SR Chowdhury, S Kumar, GS Kumar. (2008), J. Molecular Structure Vol. 891, Issues 1-3, Pages 498-507. Impact 1.599

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How to Sketch a Molecule from Scratch: Part-1

It is often necessary in various scientific disciplines to prepare sketches of molecules for project reports, research papers and teaching assignments, etc. Drawing a sketch also helps in developing the concepts in science, for example, the bonding patter in organic molecules, their valencies, etc. Educators and researchers regularly use sketches in their daily work. With the development of computing computer based sketching has become more  common and more and more people are using computers for everything for drug design, manufacturing and publications of results. Several tools are available for sketching. Here, we will see how small molecules can be drawn using an exciting and free software ‘ACDChem Sketch’ from ACD Labs. Lets begin by drawing a simple molecule ‘Indole’. The pictures below are self explaining.



You can build a larger molecule by adding side chains at the desired positions on the main Indole ring. The method is shown below.

Apart from building simpler molecule like indole…

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