Research interests

in areas of structural bioinformatics of RNA; electronic structure and properties, molecular modeling and molecular dynamics of biological systems

Education:

• Ph. D. 1980 Chemistry Indian Inst Tech (IIT) Kanpur
• Thesis advisor: Prof M. V. George
• Title: Thermal and photochemical transformations of a few azaheterotrienes and related studies
• M. Sc. 1973 I class (1st Rank) Indian Inst Tech (IIT) Kanpur
• B. Sc. (Hons) 1971 I class (2nd Rank) Indian Inst Tech (IIT) Kharagpur
• Higher Secondary 1968 I class (5th Rank) WB Board of Secondary Education

Employment:

• 2005 Professor, IIIT- Hyderabad
• 2002 Associate Professor, IIIT- Hyderabad
• 1991 Reader, Christ Church College, CSJM Kanpur University, Kanpur
• 1978 Lecturer, Christ Church College, CSJM Kanpur University, Kanpur

Visits/Additional training:

• Institut für Organische Chemie, Universität München, Germany (February 1984 – January 1986)
• Summer visiting teacher fellowship of the Indian Academy of Sciences (May – July, 2000) at NCBS Bangalore

Awards:

• National Science Talent Search Scholarship (1968-77)
• Alexander von Humboldt Research Fellowship (1984-1986)

Publications:

1. Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: Crystal structure analysis, optimal structures and accurate interaction energies: Preethi P Seelam, Abhijit Mitra and Purshotam Sharma 2019 RNA Published in advance July 17, doi:10.1261/rna.071530.119; Abstract
2. Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches: Antarip Halder, Dhruv Data, Preethi P. Seelam, Dhananjay Bhattacharyya and Abhijit Mitra 2019 ACS Omega 4, 7354-7368, doi: 10.1021/acsomega.8b03689; Full Text
3. Unfolding Transitions of Peripheral Subunit Binding Domains Show Cooperative Behavior: Monika Sharma, Gopalakrishnan Bulusu, Abhijit Mitra 2019 J. Phys. Chem. B 123, 3441-3451, doi: 10.1021/acs.jpcb.9b01114; Abstract
4. Evidence for Hidden Involvement of N3-Protonated Guanine in RNA Structure and Function.: Antarip Halder, Saurabh Vemuri, Rohit Roy, Jayanth Katuri, Dhananjay Bhattacharyya, Abhijit Mitra 2019 ACS Omega 4, 699-709, doi: 10.1021/acsomega.8b02908 Full Text
5. Going beyond base-pairs: topology-based characterization of base-multiplets in RNA.: Sohini Bhattacharya, Ayush Jhunjhunwala, Antarip Halder, Dhananjay Bhattacharyya, Abhijit Mitra 2019 RNA 25: 573-589, doi: 10.1261/rna.068551.118 Abstract
6. Consequences of Mg2+ binding on the geometry and stability of RNA base pairs: Antarip Halder, Rohit Roy, Dhananjay Bhattacharyya and Abhijit Mitra 2018 Phys. Chem. Chem. Phys. 123, 3441−3451, doi: 10.1021/acs.jpcb.9b01114; Abstract
7. Higher order structures involving post transcriptionally modified nucleobases in RNA: Seelam PP, Sharma P and Mitra A 2017 Rsc Adv. 7, 35694 -35703 doi:10.1039/C7RA05284G; Full Text
8. How does Mg²⁺ modulate the RNA folding mechanism: A case study of the G:C W:W Trans basepair: Antarip Halder, Rohit Roy, Dhananjay Bhattacharyya and Abhijit Mitra 2017 Biophysical J. 113, 1–13, doi: 10.1016/j.bpj.2017.04.029; Abstract
9. Structural landscape of base pairs containing post-transcriptional modifications in RNA: Seelam PP, Sharma P and Mitra A 2017 RNA 23 (6), 847-859 doi: 10.1261/rna.060749.117.; Abstract
10. Effects of point mutations on the thermostability of B. subtilis lipase: investigating nonadditivity: Bipin Singh, Gopalakrishnan Bulusu, and Abhijit Mitra 2016 J. Comput. Aided Mol. Des. 30:899–916; Full Text
11. The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs: Antarip Halder, Sohini Bhattacharya,  Ayan Datta, Dhananjay Bhattacharyya  and Abhijit Mitra 2015 Phys. Chem. Chem. Phys., 17(39), 26249-26263.; Abstract
12. RNABP COGEST: a resource for investigating functional RNAs: Sohini Bhattacharya, Shriyaa Mittal, Swati Panigrahi, Purshotam Sharma, Preethi S. P., Rahul Paul, Sukanya Halder, Antarip Halder, Dhananjay Bhattacharyya, and Abhijit Mitra 2015 Database, DOI: 10.1093/database/bav011; Full Text
13. Understanding the Thermostability and Activity of Bacillus subtilis Lipase Mutants: Insights from Molecular Dynamics Simulations: Bipin Singh, Gopalakrishnan Bulusu, and Abhijit Mitra 2015 J. Phys. Chem. B 119: 392-409; Abstract
14. Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study: Antarip Halder, Sukanya Halder, Dhananjay Bhattacharyya and Abhijit Mitra 2014 Phys. Chem. Chem. Phys. 16, 18383 – 18396; Abstract
15. Why Does Substitution of Thymine by 6-Ethynylpyridone Increase the Thermostability of DNA Double Helices?: Antarip Halder, Ayan Datta,, Dhananjay Bhattacharyya, and Abhijit Mitra 2014 J. Phys. Chem. B 118: 6586−6596; Abstract
16. RNA Structural Bioinformatics: Sohini Bhattacharya, Eshita Mutt, and Abhijit Mitra 2013 Proceedings of Andhra Pradesh Akademi of Sciences 15 3 : 101−124; Full Text
17. Search for Protein Sequence Homologues that Display Considerable Domain Length Variations: Eshita Mutt, Abhijit Mitra and R. Sowdhamini, 2012 International Journal of Knowledge Discovery in Bioinformatics (IJKDB), 2(2), 55-77. doi:10.4018/jkdb.2011040104, http://www.igi-global.com/article/search-protein-sequence-homologues-display/62301; Full Text
18. Mining protein sequence databases for remote homologues that can display considerable domain length variations: Eshita Mutt, Abhijit Mitra and R. Sowdhamini, 2011 11th IEEE International Conference on Data Mining Workshops, DOI 10.1109/ICDMW.2011.122, ; Full Text
19. Protonation of Base Pairs in RNA: Context Analysis and Quantum Chemical Investigations of Their Geometries and Stabilities: Mohit Chawla, Purshotam Sharma, Sukanya Halder, Dhananjay Bhattacharyya and Abhijit Mitra 2011 J. Phys.Chem. B, 115(6): 1469–1484.; Abstract
20. On the Role of cis Hoogsteen : Sugar Edge Family of Base Pairs in Platforms and Triplets – Quantum Chemical Insights into RNA Structural Biology: Pushotam Sharma, Jiří Šponer, Judit E. Šponer, Sitansh Sharma, Dhananjay Bhattacharyya, Abhijit Mitra 2010 J. Phys.Chem. B, 114(9): 3307–3320.; Abstract
21. On the Role of Hoogsteen:Hoogsteen Interactions in RNA – Ab Initio Investigations of Structures and Energies: Pushotam Sharma, Mohit Chawla, Sitansh Sharma and Abhijit Mitra 2010 RNA, 16: 942-95; Abstract
22. A Theoretical Study on Interaction of Small Gold Clusters Aun (n = 4, 6, 8) with xDNA Base Pairs: Pushotam Sharma, Sitansh Sharma, Abhijit Mitra and Harjinder Singh 2009 J Biomol Struct. Dyn., 27, 65- 82; Abstract
23. MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch: Monika Sharma, Gopalakrishnan Bulusu and Abhijit Mitra 2009 RNA 15, 1673-1692; Abstract
24. Trans Hoogsteen/Sugar Edge Base Pairing in RNA. Structures, Energies, and Stabilities from Quantum Chemical Calculations: Arnošt Mládek, Purshotam Sharma, Abhijit Mitra, Dhananjay Bhattacharyya, Jiří Šponer and Judit E. Šponer 2009 J.Phys.Chem.B, 113(6):1743-55; Abstract
25. Modeling the Noncovalent interactions at the metabolite binding site in purine riboswitches: Purshotam Sharma, Sitansh Sharma, Mohit Chawla and Abhijit Mitra 2009 J. Mol. Model. 15(6), 633-49; Full Text
26. Comparative Modeling of Thioredoxin Glutathione Reductase from Schistosoma mansoni: A Multifunctional Target for Antischistosomial therapy: Monika Sharma, Smriti Khana, Gopalakrishnan Bulusu and Abhijit Mitra 2009 J. Mol. Graph. Model., 27(6),665-675; Full Text
27. Noncanonical Base Pairing in RNA: Topological and NBO Analysis of Hoogsteen Edge - Sugar Edge Interactions: Purshotam Sharma, Harjinder Singh and Abhijit Mitra 2008 ICCS 2008 proceedings published as Lecture Notes in Computer Science LNCS Part II, 5102, 379-386; Full Text
28. Quantum chemical studies of structures and interaction energies of RNA base pair: The Trans Watson Crick-Watson-Crick family: Purshotam Sharma, Abhijit Mitra, Sitansh Sharma, Harjinder Singh and Dhananjay Bhattacharyya 2008 J Biomol Struct. Dyn., 25, 709-732; Abstract
29. Theoretical analysis of noncanonical base pairing interactions in RNA molecules; Dhananjay Bhattacharyya, Siv Chand Koripella, Abhijit Mitra, Vijay Babu Rajendran and Bhabdyuti Sinha 2007 J Biosci. 32(5) 809-825; Full Text
30. Base pairing in RNA: A computational analysis of structural aspects and interaction energie; Purshotam Sharma, Abhijit Mitra, Sitansh Sharma and Harjinder Singh 2007 J. Chem. Sci. 119(5) 525-531; Full Text
31. Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis; Jhuma Das, Shayantani Mukherjee, Abhijit Mitra and Dhananjay Bhattacharyya 2006 J Biomol Struct. Dyn., 24 149-162; Abstract

1. The reaction of aliphatic diazo compounds with highly electrophilic ethylene derivatives. Ulrich Eichenauer, Rolf Huisgen, Abhijit Mitra and Joaquin Rodriguez Moran, Heterocycles, 25, 129 (1987)
2. 1, 3-Dipolare Cycloadditionen 92 Reactionen aliphatischerdiazoverbindungen mit vierfach acceptor substituerten ethylenen. , Rolf Huisgen, Ulrich Eichenauer, Elke Langhals, Abhijit Mitra and Joaquin Rodriguez Moran, Chemische Berichte, 120, 153 (1987).; Abstract
3. 1, 3-Dipolare Cycloadditionen 93. Ueberraschungen bei der umsetzung des 2, 3-dicyanfumarsaeuere dimethylesteres mit diazomethane, Rolf Huisgen, Abhijit Mitra and Joaquin Rodriguez Moran, Chemische Berischte, 120, 159 (1987).; Abstract
4. The Surprising reaction of diazomethane with dimethyl 2, 3-dicyanofumarate, Rolf Huisgen, Abhijit Mitra and Joaquin Rodriguez Moran, Heterocycles, 24, 2429 (1986).
5. Review : Thermal and photochemical transformations of hetro-1,3,5-hexatrienes into five –membered rings – possible pericyclic reactions, Manaparathu V. George, Abhijit Mitra and Kutikat B Sukumaran, Angew. Chem Internat.Ed. Engl. 19,973(1980).; Abstract
6. Thermal and Photochemical transformations of 1-(arylazo)-N-arylidene-2-naphthylamines, Abhijit Mitra, Shiv M.S. Chauhan and M.V. George, J.Org. Chem.,35,3182(1980); Abstract
7. Reaction of 3,6-diphenyl-1,2,4,5-tetrazine with cis,cis-1,5-cyclooctadiene attempt at preparing some dihydropyridazine derivatives, S. Satish, A. Mitra and M.V. George, Tetrahedron, 35, 77 (1979); Abstract

• An Experiment on Introducing Human Values Course in Undergraduate Curriculum of Engineering Education, Ramancharla Pradeep Kumar, Rajeev Sangal, Abhijit Mitra, Navjyoti Singh, Kamalakar Karlapalem, 2009 Northeast American Society of Engineering Education Conference, April 03-04,2009 University of Bridgeport.; Full Text
• The Nexus Between Computers and Modern Biology: The Changing Face of Scientific Research, Abhijit Mitra, Proceedings of "Computer Applications for the 21st century: Synergies and Vistas" 11-12 December 2008, Vidyasagar College, Kolkata Conference Sponsored by UGC, DST and CFSL,Full Text

Research projects awarded by DBT

Four completed

1. BT/PR14715/PBD/16/903/2010: “Computational Core for Plant Metabolomics“
2. BT/PR-11429/BID/07/272/2008: “In silico understanding of structures, stability and dynamics of RNA riboswitches — energetics and MD simulations using QM and MM methods”
3. BT/PR5767/PID/06/260/2005: “Development of Biosensor for Infectious Diseases”
4. BT/PR5451/07/111/2004: “Database of Quantum Chemical Interaction Energy and Geometric Meta Data for Non Canonical Base Pairs in Functional RNA Structures”

Supervision of Ph.D students: Eight graduated, three in progress

Thesis titles of graduated PhD students:

1. Quantum Chemical Studies of Structures and Stabilities of Natural and Synthetic Nucleic Acid Systems: Electronic Structure Analysis of Noncovalent Interactions in Functional RNA and Modified DNA, Purshotam Sharma, May 2011. Advisor: Abhijit Mitra, Harjinder Singh
2. Genome organization and regulation: Role of non-coding elements and epigenetic components, Senthilkumar Ramamoorthy, June 2011, Advisor: Rakesh Kumar Mishra, Abhijit Mitra
3. Dynamics of Nucleic Acids and Proteins: Investigations of some contemporary issues, Monika Sharma, June 2012, Advisor: Abhijit Mitra, Harjinder Singh
4. Length variation analysis of protein domain superfamilies amongst sequence homologues, Eshita Mutt, July 2014, Abhijit Mitra, R Sowdhamini
5. Understanding the differences in preliminary stages of gene expression regulation in healthy and unhealthy mammalian tissues, and identification of potential markers, Neelima Ch, November 2016. Advisor: Abhijit Mitra, Kshitish Acharya
6. Understanding the molecular basis of thermostability and activity of B. subtilis lipase and its mutants, Bipin Singh, March 2017. Advisor: Abhijit Mitra, B. Gopalakrishnan
7. Molecular level understanding of modified base pairs, Nucleobase-Ligand pseudo pairs and associated higher order structures in functional RNA, Preethi S P, March 2018. Advisor: Abhijit Mitra
8. On the diverse roles of nucleobases in shaping RNA structures and functions - a QM based insight, Antarip Halder, June 2018. Advisor: Abhijit Mitra, Dhananjay Bhattacharyya

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