BioPhysics: (12)
  1. I. Ghosh and V. S. R. Rao, “A conformational approach to the study of the dynamics of enzyme inhibition: studies on thermolysin,” Int. J. Biol. Macromol., vol. 4, no. 3, pp. 130–136, 1982.
  2. I. Ghosh and V. S. R. Rao, “Effect of Configuration of the Inhibitors on the Mode of Binding to the Enzyme, Thermolysin,” J. Biomol. Struct. Dyn., vol. 2, no. 1, pp. 29–40, 1984.
  3. T. P. Lybrand, I. Ghosh, and J. A. McCammon, “Hydration of chloride and bromide anions: determination of relative free energy by computer simulation,” J. Am. Chem. Soc., vol. 107, no. 25, pp. 7793–7794, 1985.
  4. I. Ghosh and J. A. McCammon, “Sidechain rotational isomerization in proteins. Dynamic simulation with solvent surroundings,” Biophys. J., vol. 51, no. 4, pp. 637–641, 1987.
  5. I. Ghosh and J. A. McCammon, “Solvent viscosity effects on the rate of side-chain rotational isomerization in a protein molecule,” J. Phys. Chem., vol. 91, no. 19, pp. 4878–4881, 1987.
  7. O. Edholm and I. Ghosh, “Hysteresis and statistical errors in free energy perturbation L to D amino acid conversion,” Mol. Simul., vol. 10, no. 2“6, pp. 241–253, 1993.
  8. I. Ghosh and O. Edholm, “Molecular dynamics study of the binding of phenylalanine stereoisomers to thermolysin,” Biophys. Chem., vol. 50, no. 3, pp. 237–248, 1994.
  9. D. Sarkar, I. Ghosh, and S. Datta, “Biochemical characterization of Plasmodium falciparum hypoxanthine-guanine-xanthine phosphorybosyltransferase: Role of histidine residue in substrate selectivity,” Mol. Biochem. Parasitol., vol. 137, no. 2, pp. 267–276, 2004.
  10. J.-N. Gillet and I. Ghosh, “Concepts on the protein folding problem,” J. Biomol. Struct. Dyn., vol. 31, no. 9, pp. 1020–1023, 2013.
  11. S. K. Panday, M. Sturlese, V. Salmaso, I. Ghosh, and S. Moro, “Coupling Supervised-MD (SuMD) with Entropy Estimations To Shine A Light On The Stability of Multiple Binding Sites.,” ACS Med. Chem. Lett., vol. 10, no. 4, pp. 444–449, 2019.
  12. S. K. Panday, and I. Ghosh, “Application and Comprehensive Analysis of Neighbor Approximated Information Theoretic Configurational Entropy Methods to Protein–Ligand Binding Cases” J. Chem. Theory Comput., vol. xx, no. x, pp. xxx–xxx, 2020. DOI: 10.1021/acs.jctc.0c00764.
Bioinformatics/Computational & Systems Biology (29)
  1. S. Datta, W. H. Li, I. Ghosh, C. C. Luo, and L. Chan, “Structure and expression of dog apolipoprotein C-II and C-III mRNAs. Implications for the evolution and functional constraints of apolipoprotein structure,” J. Biol. Chem., vol. 262, no. 22, pp. 10588–10593, 1987.
  2. I. Ghosh, “Mapping of T-cell epitopes with the help of accessible surface area,” J. Mol. Graph., vol. 8, no. 4, p. 229, 2002.
  3. I. Ghosh, “Designing a small peptide toxin using molecular dynamics,” J. Mol. Graph., vol. 11, no. 1, p. 62, 2002.
  4. N. Campillo, H. A. Nagarajaram, and I. Ghosh, “Phosphoribosyltransferase superfamily: A comparative structural analysis,” J. Mol. Model., vol. 7, no. 4, pp. 80–89, 2001.
  5. V. K. Singh and I. Ghosh, “Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets,” Theor. Biol. Med. Model., vol. 3, 2006.
  6. A. Banerji and I. Ghosh, “A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in proteins,” Eur. Biophys. J., vol. 38, no. 5, pp. 577–587, 2009.
  7. A. Hosseini, S. H. Ranade, I. Ghosh, and P. Khandekar, “Simple sequence repeats in different genome sequences of Shigella and comparison with high GC and AT-rich genomes: Full Length Research Paper,” DNA Seq., vol. 19, no. 3, pp. 167–176, 2008.
  8. R. Vinekar and I. Ghosh, “Determination of phosphorylation sites for nadp-specific isocitrate dehydrogenase from mycobacterium tuberculosis,” J. Biomol. Struct. Dyn., vol. 26, no. 6, pp. 741–754, 2009.
  9. A. Banerji and I. Ghosh, “Revisiting the myths of protein interior: Studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions,” PLoS One, vol. 4, no. 10, 2009.
  10. A. Kumar and I. Ghosh, “Mapping selectivity and specificity of active site of plasmepsins from Plasmodium falciparum using molecular interaction field approach,” Protein Pept. Lett., vol. 14, no. 6, pp. 569–574, 2007.
  11. A. Borkar, I. Ghosh, and D. Bhattacharyya, “Structure and dynamics of double helical DNA in torsion angle hyperspace: A molecular mechanics approach,” J. Biomol. Struct. Dyn., vol. 27, no. 5, pp. 695–712, 2010.
  12. A. Banerji and I. Ghosh, “Mathematical criteria to observe mesoscopic emergence of protein biochemical properties,” J. Math. Chem., vol. 49, no. 3, pp. 643–665, 2011.
  13. I. Ghosh, “Proteins will Fold Anyway!!,” J. Biomol. Struct. Dyn., vol. 28, no. 4, pp. 627–628, 2012.
  14. A. Banerji and I. Ghosh, “Fractal symmetry of protein interior: what have we learned?,” Cell. Mol. Life Sci., vol. 68, no. 16, pp. 2711–2737, 2011.
  15. N. Biyani, S. Mandal, C. Seth, M. Saint, K. Natarajan, I. Ghosh, and R. Madhubala, “Characterization of leishmania donovani aquaporins shows presence of subcellular aquaporins similar to tonoplast intrinsic proteins of plants,” PLoS One, vol. 6, no. 9, 2011.
  16. U. Sarma, A. Sareen, M. Maiti, V. Kamat, R. Sudan, S. Pahari, N. Srivastava, S. Roy, S. Sinha, I. Ghosh, and others, “Modeling and experimental analyses reveals signaling plasticity in a bi-modular assembly of CD40 receptor activated kinases,” PLoS One, vol. 7, no. 7, p. e39898, 2012.
  17. U. Sarma and I. Ghosh, “Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops,” BMC Res. Notes, vol. 5, no. 1, p. 287, 2012.
  18. U. Sarma and I. Ghosh, “Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade,” BMC Syst. Biol., vol. 6, no. 1, p. 82, 2012.
  19. R. Vinekar, C. Verma, and I. Ghosh, “Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases,” BMC bioinformatics, vol. 13, no. 17, p. S2, 2012.
  20. A. Hosseini, S. Dutta, S. Nandy, I. Ghosh, and P. S. Khandekar, “Characterization of Shigella flexneri Isolates by Tandem Repeat Analysis and Pulsed-Field Gel Electrophoresis,” Int Prof Chem. Biol. Env. Engg, vol. 46, p. 110, 2012.
  21. V. S. Gowri, I. Ghosh, A. Sharma, and R. Madhubala, “Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major,” BMC Genomics, vol. 13, no. 1, p. 621, 2012.
  22. H. Ashraf, I. Ghosh, P. Khandekar, and M. H. Ayoubian, “Simple sequence repeats in specific gene groups of shigella genome,” IIOAB J., vol. 4, no. 1, pp. 17–24, 2013.
  23. V. K. Singh and I. Ghosh, “Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum,” FEBS Lett., vol. 587, no. 17, pp. 2806–2817, 2013.
  24. A. Shandilya, S. Chacko, B. Jayaram, and I. Ghosh, “A plausible mechanism for the antimalarial activity of artemisinin: a computational approach,” Sci. Rep., vol. 3, p. 2513, 2013.
  25. T. Khan and I. Ghosh, “Modularity in protein structures: study on all-alpha proteins,” J. Biomol. Struct. Dyn., vol. 33, no. 12, pp. 2667–2681, 2015.
  26. T. Khan and I. Ghosh, “173 Topological variance in protein structure: an insight from kinetics and functional study,” J. Biomol. Struct. Dyn., vol. 33, no. sup1, pp. 113–114, 2015.
  27. R. Kaalia and I. Ghosh, “Semantics based approach for analyzing disease-target associations,” J. Biomed. Inform., vol. 62, pp. 125–135, 2016.
  28. R. Bansal, H. Bhusan Samal, V. S. Gowri, S. Sankar Sen, I. Ghosh, and R. Madhubala, “The cytochrome P450 complement (CYPome) of leishmania leads to the discovery of a plant like cytochrome P450 sub-family CYP710C1 gene,” Proc. Indian Natl. Sci. Acad., vol. 83, no. 3, pp. 701–715, 2017.
  29. G. Das, S. Das, S. Dutta, and I. Ghosh, “In silico identification and characterization of stress and virulence associated repeats in Salmonella,” Genomics, vol. 110, no. 1, pp. 23–34, 2018.
Development of program/SW/Databases: (9)
  1. N. V. Ramana and I. Ghosh, “Software report: Molecular graphics software-MOGRA,” Comput. Graph., vol. 17, no. 4, pp. 415–416, 1993.
  2. I. Mahadevan and I. Ghosh, “Analysis of E.coli promoter structures using neural networks,” Nucleic Acids Res., vol. 22, no. 11, pp. 2158–2165, 1994.
  3. M. A. Mukund, T. Bannerjee, I. Ghosh, and S. Datta, “Effect of mRNA secondary structure in the regulation of gene expression: Unfolding of stable loop causes the expression of Taq polymerase in E. coli,” Curr. Sci., vol. 76, no. 11, pp. 1486–1490, 1999.
  4. M. A. L. Anto, G. Gopakumar, A. S. Nair, and I. Ghosh, “GENFOCS: A Comparative Tool on Gene Finding with Sensitivity and Specificity,” in Bioinformatics Research and Development, pp. 509–516, 2008.
  5. R. Prabha, I. Ghosh, and D. P. Singh, “Plant Stress Gene Database?: A Collection of Plant Genes Responding to Stress Condition,” J. Sci. Technol., vol. 1, no. 1, pp. 28–31, 2012.
  6. A. Kumar, N. Agarwal, L. Pant, J. P. Singh, I. Ghosh, and N. Subbarao, “PfalDB: an integrated drug target and chemical database for Plasmodium falciparum,” Curr. Drug Targets, vol. 15, no. 12, pp. 1089–93, 2014.
  7. P. Kumar, G. Das, and I. Ghosh, “Critical Assessment of Contribution from Indian Publications: The Role of In Silico Designing Methods Leading to Drugs or Drug-Like Compounds Using Text Based Mining and Association,” J. Proteins Proteomics, vol. 8, no. 3, pp. 133–148, 2017.
  8. V. Pudi, P. Rani, A. Mitra, and I. Ghosh, “Computational core for plant metabolomics: A case for interdisciplinary research,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 10721 LNCS, pp. 223–234, 2017.
  9. T. Khan, S. K. Panday, and I. Ghosh, “ProLego: Tool for extracting and visualizing topological modules in protein structures,” BMC Bioinformatics, vol. 19, no. 1, 2018.
Chemoinformatics & Drug design: (10)
  1. C. Raychaudhury and I. Ghosh, “An information-theoretical measure of similarity and a topological shape and size descriptor for molecular similarity analysis,” Internet Electron. J. Mol. Des, vol. 3, pp. 350–360, 2004.
  2. H. A. Nagarajaram, P. Iengar, and I. Ghosh, “In silico approach to antimalarial drug discovery: Design of selective inhibitor to Plasmodium falciparum aspartic proteases,” Front. Biophys., vol. 6, pp. 168–181, 2005.
  3. I. Ghosh, “Target based high throughput screening and lead designing in pharmaceutical drug industry,” Indian J. Chem. - Sect. A Inorganic, Phys. Theor. Anal. Chem., vol. 45, no. 1, pp. 163–173, 2006.
  4. O. Prakash and I. Ghosh, “Developing an antituberculosis compounds database and data mining in the search of a motif responsible for the activity of a diverse class of antituberculosis agents,” J. Chem. Inf. Model., vol. 46, no. 1, pp. 17–23, 2006.
  5. I. Ghosh, S. Ray, and O. P. Pandey, “In search of maximum common substructure responsible for toxicity,” Toxicol. Lett., vol. 189, p. S263, 2009.
  6. N. Puri, O. Prakash, R. Manoharlal, M. Sharma, I. Ghosh, and R. Prasad, “Analysis of physico-chemical properties of substrates of ABC and MFS multidrug transporters of pathogenic Candida albicans,” Eur. J. Med. Chem., vol. 45, no. 11, pp. 4813–4826, 2010.
  7. B. Hardy, N. Douglas, C. Helma, M. Rautenberg, N. Jeliazkova, V. Jeliazkov, I. Nikolova, R. Benigni, O. Tcheremenskaia, S. Kramer, T. Girschick, F. Buchwald, J. Wicker, A. Karwath, M. Gütlein, A. Maunz, H. Sarimveis, G. Melagraki, A. Afantitis, P. Sopasakis, D. Gallagher, V. Poroikov, D. Filimonov, A. Zakharov, A. Lagunin, T. Gloriozova, S. Novikov, N. Skvortsova, D. Druzhilovsky, S. Chawla, I. Ghosh, S. Ray, H. Patel, and S. Escher, “Collaborative development of predictive toxicology applications,” J. Cheminform., vol. 2, no. 7, 2010.
  8. R. Kaalia, A. Kumar, A. Srinivasan, and I. Ghosh, “An Ab Initio Method for Designing Multi-Target Specific Pharmacophores using Complementary Interaction Field of Aspartic Proteases,” Mol. Inform., vol. 34, no. 6–7, pp. 380–393, 2015.
  9. R. Kaalia, A. Srinivasan, A. Kumar, and I. Ghosh, “ILP-assisted de novo drug design,” Mach. Learn., vol. 103, no. 3, pp. 309–341, 2016.
  10. P. Kumar, R. Kaalia, A. Srinivasan, and I. Ghosh, “Multiple target-based pharmacophore design from active site structures” SAR QSAR Environ. Res., vol. 29, no. 1, pp. 1–19, 2018.
  1. M. S. Rao and I. Ghosh, “Modelling the binding of moenomycin and its fragments to the active site of transglycosylase enzyme model”, in JOURNAL OF MOLECULAR GRAPHICS & MODELLING, vol. 16, no. 4–6, pp. 296–297, 1998.
  2. Target Identification using Phylogenetic Profiling, Prachi Deshpande, Indira Ghosh (not listed)
  3. A. Banerji and I. Ghosh, “Criteria to observe mesoscopic emergence of protein biophysical properties,” arXiv Prepr. arXiv0907.0073, 2009.
Book Chapters (9)
  1. Indira Ghosh, “Side chain ....... study.” in Spectroscopy of Biological Molecules New Advances. ed. By E.D.Schmid, F.W.Schneider & F.Siebert, 39–42, John Wiley & sons, 1988.
  2. Subhash Choudhary, Ananta Paine and Indira Ghosh “Application of Bioinformatics in Drug designing in Antimalarial Drug Targets” published as a chapter in the book “Current Trends in Pharmacology” ed. A.Ray & K.Gulati, IK publishing house, New Delhi. 2007.
  3. Kushwaha HR, Ghosh I, Pareek A. “General overview of bioinformatics tools in agricultural sciences” in Biotechnology in agricluture and medicine: Principles & Practice. ed. Gupta AK, Pareek A, Gupta SM.(I. K. International, INDIA), 2011.
  4. Kushwaha Hemant Ritturaj and Ghosh Indira. “Target Identification using Systems Approach in Infectious Diseases” , in TRANSLATIONAL RESEARCH IN NEW DRUG DEVELOPMENT. Ed. Ray Arunabha & Gulati Kavita (V.P, India), 2012.
  5. Kushwaha Hemant Ritturaj and Ghosh Indira , “Bioinformatics Approach for Finding Target Protein in Infectious Disease” , in Bioinformatics of Human Proteomics, Translational Bioinformatics 3, DOI 10.1007/978-94-007-5811-7_10, X. Wang (ed.), Springer Science+Business Media Dordrecht 2013.
  6. A. Banerji, and I. Ghosh, “Effectiveness of Fractal Dimension based Measures to Investigate Protein Structures” in Biomolecular Forms and Functions, Ed. M. Bansal, N. Srinivasan, pp. 482–491, 2013.
  7. Pawan K., Shandilya A., Jayaram B., Ghosh I., “Integrative Method for Finding Antimalarials Using In Silico approach” in Computer Design for new drugs and materials. Chapter 2 pp. 13-38. New York NY, Nova Science Publishers, 2016.
  8. Pawan Kumar and Indira Ghosh , “Application of in silico Drug Repurposing in Infectious Disease”, in the book “In Silico Drug Design: Repurposing Techniques and Methodologies” edited by Kunal Roy and online available Feb 2019 published by Academic Press & Elsevier, 2019. ISBN 978-0-12-816125-8.
  9. Shailesh K. Panday and Indira Ghosh, “In-silico structure based prediction of receptor-ligand binding affinity: current progress and challenges” in the book “Structural Bioinformatics: Applications in Preclinical Drug Discovery Process” edited by C.GopiMohan and published by Springer, Jan 2019.
  1. Copyright on the Graphics SW MOGRA, developed by Ms. N.V.Ramana and Indira Ghosh has been done in 1992.
  2. A patent application in the category of “New Patent Application” has been granted in UK, Jun 2005 on behalf of AstraZeneca, on the TB associated target for drug design “METHOD - Patent - for attenuating a microorganism which comprises inhibiting in the microorganism a metabolic pathway essential for viability” IPN:WO2004/087943 A1.