Abhijit Mitra

Professor
Center for Computational Natural Sciences and Bioinformatics
International Institute of Information Technology, Hyderabad, TS 500032

Ph: +91-40-66531171(O)); +91-40-66531201(R); +91-9866406028(mobile); +91-40-66531413(fax-O);
email: abi_chem@iiit.ac.in

Research interests
in areas of structural bioinformatics of RNA; electronic structure and properties, molecular modeling and molecular dynamics of biological systems
Research profile
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Education:


Employment:

Visits/Additional training:

Awards:


Publications:

  • List of selected recent publications:

    1. 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
    2. 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
    3. 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
    4. 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
    5. 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
    6. 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
    7. 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
    8. 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
    9. 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
    10. RNA Structural Bioinformatics: Sohini Bhattacharya, Eshita Mutt, and Abhijit Mitra 2013 Proceedings of Andhra Pradesh Akademi of Sciences 15 3 : 101−124; Abstract
    11. 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
    12. 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
    13. 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
    14. 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
    15. 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
    16. 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
    17. 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
    18. 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
    19. 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
    20. 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
    21. 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
    22. 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
    23. 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
    24. 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
    25. 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
    Several abstracts in proceedings of several national and international conferences.

    List of earlier publications:
    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
  • List of other publications:


  • Research projects awarded by DBT

    One ongoing:

  • BT/PR14715/PBD/16/903/2010: “Computational Core for Plant Metabolomics

  • Three completed
    1. 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
    2. BT/PR5767/PID/06/260/2005: “Development of Biosensor for Infectious Diseases
    3. 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: Six graduated, four 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
    Supervision of M.S by Research students: twelve graduated and six in progress


    Personal:

  • Date of Birth: July 23, 1952, born and brought up in Kolkata
  • Marital status: Married with two children

  • Last updated on: August 2017