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  • Pal, S., Pal, A., and Mohanty, D. (2025). SG‐ML‐PLAP: A structure‐guided machine learning–based scoring function for protein–ligand binding affinity prediction. Protein Science, 34(1), e5257. doi: 10.1002/pro.5257
  • Khanduja, A., M. Kumar, and D. Mohanty. 2023. “ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes.” Brief Bioinform. doi: 10.1093/bib/bbad101.
  • Mehdiratta, K., S. Nain, M. Sharma, S. Singh, S. Srivastava, B.D. Dhamale, D. Mohanty, S.S. Kamat, V.T. Natarajan, R. Sharma, and R.S. Gokhale. 2022. “Respiratory Quinone Switches from Menaquinone to Polyketide Quinone during the Development Cycle in Streptomyces sp. Strain MNU77.” Microbiol Spectr:e0259722. doi: 10.1128/spectrum.02597-22.
  • Gupta, P., and D. Mohanty. 2022. “Allosteric regulation of the inactive to active state conformational transition in CDPK1 protein of Plasmodium falciparum.” Int J Biol Macromol 215:489-500. doi: 10.1016/j.ijbiomac.2022.06.065.
  • Gupta, P., S. Venkadesan, and D. Mohanty. 2022. “Pf-Phospho: a machine learning-based phosphorylation sites prediction tool for Plasmodium proteins.” Brief Bioinform 23 (4). doi: 10.1093/bib/bbac249.
  • Mehdiratta, K., S. Singh, S. Sharma, R.S. Bhosale, R. Choudhury, D.P. Masal, A. Manocha, B.D. Dhamale, N. Khan, V. Asokachandran, P. Sharma, M. Ikeh, A.C. Brown, T. Parish, A.K. Ojha, J.S. Michael, M. Faruq, G.R. Medigeshi, D. Mohanty, D.S. Reddy, V.T. Natarajan, S.S. Kamat, and R.S. Gokhale. 2022. “Kupyaphores are zinc homeostatic metallophores required for colonization of Mycobacterium tuberculosis.” Proc Natl Acad Sci U S A 119 (8). doi: 10.1073/pnas.2110293119.
  • Kumar, P., and D. Mohanty. 2022. “Development of a Novel Pharmacophore Model Guided by the Ensemble of Waters and Small Molecule Fragments Bound to SARS-CoV-2 Main Protease.” Mol Inform 41 (2):e2100178. doi: 10.1002/minf.202100178.
  • Gupta, P., and D. Mohanty. 2021. “SMMPPI: a machine learning-based approach for prediction of modulators of protein-protein interactions and its application for identification of novel inhibitors for RBD:hACE2 interactions in SARS-CoV-2.” Brief Bioinform 22 (5). doi: 10.1093/bib/bbab111.
  • Agrawal, P., S. Amir, Deepak, D. Barua, and D. Mohanty. 2021. “RiPPMiner-Genome: A Web Resource for Automated Prediction of Crosslinked Chemical Structures of RiPPs by Genome Mining.” J Mol Biol 433 (11):166887. doi: 10.1016/j.jmb.2021.166887.
  • Agrawal, P., and D. Mohanty. 2021. “A machine learning-based method for prediction of macrocyclization patterns of polyketides and non-ribosomal peptides.” Bioinformatics 37 (5):603-611. doi: 10.1093/bioinformatics/btaa851.
  • Kaur, P., M. Rausch, B. Malakar, U. Watson, N.P. Damle, Y. Chawla, S. Srinivasan, K. Sharma, T. Schneider, G.D. Jhingan, D. Saini, D. Mohanty, F. Grein, and V.K. Nandicoori. 2019. “LipidII interaction with specific residues of Mycobacterium tuberculosis PknB extracytoplasmic domain governs its optimal activation.” Nat Commun 10 (1):1231. doi: 10.1038/s41467-019-09223-9.
  • Kaur, H., N. Sain, D. Mohanty, and D.M. Salunke. 2018. “Deciphering evolution of immune recognition in antibodies.” BMC Struct Biol 18 (1):19. doi: 10.1186/s12900-018-0096-1.
  • Sharma, C., and D. Mohanty. 2018. “Sequence- and structure-based analysis of proteins involved in miRNA biogenesis.” J Biomol Struct Dyn 36 (1):139-151. doi: 10.1080/07391102.2016.1269687.
  • Agrawal, P., S. Khater, M. Gupta, N. Sain, and D. Mohanty. 2017. “RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links.” Nucleic Acids Res 45 (W1):W80-W88. doi: 10.1093/nar/gkx408.
  • Khater, S., M. Gupta, P. Agrawal, N. Sain, J. Prava, P. Gupta, M. Grover, N. Kumar, and D. Mohanty. 2017. “SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases.” Nucleic Acids Res 45 (W1):W72-W79. doi: 10.1093/nar/gkx344.
  • Sharma, C., and D. Mohanty. 2017. “Molecular Dynamics Simulations for Deciphering the Structural Basis of Recognition of Pre-let-7 miRNAs by LIN28.” Biochemistry 56 (5):723-735. doi: 10.1021/acs.biochem.6b00837.
  • Sain, N., and D. Mohanty. 2016. “modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks.” Biol Direct 11 (1):48. doi: 10.1186/s13062-016-0151-4.
  • Sain, N., G. Tiwari, and D. Mohanty. 2016. “Understanding the molecular basis of substrate binding specificity of PTB domains.” Sci Rep 6:31418. doi: 10.1038/srep31418.
  • Khater, S., S. Anand, and D. Mohanty. 2016. “In silico methods for linking genes and secondary metabolites: The way forward.” Synth Syst Biotechnol 1 (2):80-88. doi: 10.1016/j.synbio.2016.03.001.
  • Khater, S., and D. Mohanty. 2015. “Deciphering the Molecular Basis of Functional Divergence in AMPylating Enzymes by Molecular Dynamics Simulations and Structure Guided Phylogeny.” Biochemistry 54 (33):5209-5224. doi: 10.1021/acs.biochem.5b00351.
  • Khater, S., and D. Mohanty. 2015. “In silico identification of AMPylating enzymes and study of their divergent evolution.” Sci Rep 5:10804. doi: 10.1038/srep10804.
  • Khater, S., and D. Mohanty. 2015. “novPTMenzy: a database for enzymes involved in novel post-translational modifications.” Database (Oxford) 2015:bav039. doi: 10.1093/database/bav039.
  • Kumar, N., N.P. Damle, and D. Mohanty. 2015. “Getting phosphorylated: is it necessary to be solvent accessible?” Proc Indian Natn Sci Acad.
  • Khater, S., and D. Mohanty. 2014. “Genome-wide search for eliminylating domains reveals novel function for BLES03-like proteins.” Genome Biol Evol 6 (8):2017-2033. doi: 10.1093/gbe/evu161.
  • Damle, N.P., and D. Mohanty. 2014. “Mechanism of autophosphorylation of mycobacterial PknB explored by molecular dynamics simulations.” Biochemistry 53 (28):4715-4726. doi: 10.1021/bi500245v.
  • Tiwari, G., and D. Mohanty. 2014. “Structure-based multiscale approach for identification of interaction partners of PDZ domains.” J Chem Inf Model 54 (4):1143-1156. doi: 10.1021/ci400627y.
  • Damle, N.P., and D. Mohanty. 2014. “Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network.” Bioinformatics 30 (12):1730-1738. doi: 10.1093/bioinformatics/btu112.
  • Tiwari, G., and D. Mohanty. 2013. “An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions.” PLoS One 8 (8):e71340. doi: 10.1371/journal.pone.0071340.
  • Yadav, G., S. Anand, and D. Mohanty. 2013. “Prediction of inter domain interactions in modular polyketide synthases by docking and correlated mutation analysis.” J Biomol Struct Dyn 31 (1):17-29. doi: 10.1080/07391102.2012.691342.
  • KHATER, S., and D. MOHANTY. 2013. “STRUCTURAL BIOINFORMATICS APPROACHES FOR DECIPHERING BIOSYNTHETIC CODE OF SECONDARY METABOLITES.” Biomolecular Forms and Functions: A Celebration of 50 Years of the Ramachandran Map:428-442.
  • Vats, A., A.K. Singh, R. Mukherjee, T. Chopra, M.S. Ravindran, D. Mohanty, D. Chatterji, J.M. Reyrat, and R.S. Gokhale. 2012. “Retrobiosynthetic approach delineates the biosynthetic pathway and the structure of the acyl chain of mycobacterial glycopeptidolipids.” J Biol Chem 287 (36):30677-30687. doi: 10.1074/jbc.M112.384966.
  • Anand, S., and D. Mohanty. 2012. “Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide synthases: a docking and molecular dynamics study.” BMC Struct Biol 12:10. doi: 10.1186/1472-6807-12-10.
  • Ahmed, A., K. Gaadhe, G.P. Sharma, N. Kumar, M. Neculai, R. Hui, D. Mohanty, and P. Sharma. 2012. “Novel insights into the regulation of malarial calcium-dependent protein kinase 1.” FASEB J 26 (8):3212-3221. doi: 10.1096/fj.12-203877.
  • De, S., J. Kumari, R. Mudgal, P. Modi, S. Gupta, K. Futami, H. Goto, N.M. Lindor, Y. Furuichi, D. Mohanty, and S. Sengupta. 2012. “RECQL4 is essential for the transport of p53 to mitochondria in normal human cells in the absence of exogenous stress.” J Cell Sci 125 (Pt 10):2509-2522. doi: 10.1242/jcs.101501.
  • Anand, S., and D. Mohanty. 2012. “Inter-domain movements in polyketide synthases: a molecular dynamics study.” Mol Biosyst 8 (4):1157-1171. doi: 10.1039/c2mb05425f.
  • Kaushik, S., D. Mohanty, and A. Surolia. 2012. “Molecular dynamics simulations on pars intercerebralis major peptide-C (PMP-C) reveal the role of glycosylation and disulfide bonds in its enhanced structural stability and function.” J Biomol Struct Dyn 29 (5):905-920. doi: 10.1080/073911012010525026.
  • Nair, D.R., S. Anand, P. Verma, D. Mohanty, and R.S. Gokhale. 2012. “Genetic, biosynthetic and functional versatility of polyketide synthases.” Current Science:277-287.
  • Nair, D.R., R. Ghosh, A. Manocha, D. Mohanty, S. Saran, and R.S. Gokhale. 2011. “Two functionally distinctive phosphopantetheinyl transferases from amoeba Dictyostelium discoideum.” PLoS One 6 (9):e24262. doi: 10.1371/journal.pone.0024262.
  • Mohanty, D., R. Sankaranarayanan, and R.S. Gokhale. 2011. “Fatty acyl-AMP ligases and polyketide synthases are unique enzymes of lipid biosynthetic machinery in Mycobacterium tuberculosis.” Tuberculosis (Edinb) 91 (5):448-455. doi: 10.1016/j.tube.2011.04.006.
  • Kaushik, S., D. Mohanty, and A. Surolia. 2011. “Role of glycosylation in structure and stability of Erythrina corallodendron lectin (EcorL): a molecular dynamics study.” Protein Sci 20 (3):465-481. doi: 10.1002/pro.578.
  • Anand, S., and D. Mohanty. 2011. “Computational methods for identification of novel secondary metabolite biosynthetic pathways by genome analysis.” In Handbook of research on computational and systems biology: Interdisciplinary applications, 380-405. IGI Global.
  • Kumar, N., and D. Mohanty. 2010. “Structure-based identification of MHC binding peptides: Benchmarking of prediction accuracy.” Mol Biosyst 6 (12):2508-2520. doi: 10.1039/c0mb00013b.
  • Kaur, S., P. Modi, V. Srivastava, R. Mudgal, S. Tikoo, P. Arora, D. Mohanty, and S. Sengupta. 2010. “Chk1-dependent constitutive phosphorylation of BLM helicase at serine 646 decreases after DNA damage.” Mol Cancer Res 8 (9):1234-1247. doi: 10.1158/1541-7786.MCR-10-0233.
  • Anand, S., M.V. Prasad, G. Yadav, N. Kumar, J. Shehara, M.Z. Ansari, and D. Mohanty. 2010. “SBSPKS: structure based sequence analysis of polyketide synthases.” Nucleic Acids Res 38 (Web Server issue):W487-496. doi: 10.1093/nar/gkq340.
  • Khurana, P., R.S. Gokhale, and D. Mohanty. 2010. “Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles.” BMC Bioinformatics 11:57. doi: 10.1186/1471-2105-11-57.
  • Kumar, N., and D. Mohanty. 2010. “Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials.” Bioinformatics 26 (2):189-197. doi: 10.1093/bioinformatics/btp633.
  • Sharma, D., D. Mohanty, and A. Surolia. 2009. “RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways.” Nucleic Acids Res 37 (Web Server issue):W193-201. doi: 10.1093/nar/gkp388.
  • Yadav, G., R.S. Gokhale, and D. Mohanty. 2009. “Towards prediction of metabolic products of polyketide synthases: an in silico analysis.” PLoS Comput Biol 5 (4):e1000351. doi: 10.1371/journal.pcbi.1000351.
  • Arora, P., A. Goyal, V.T. Natarajan, E. Rajakumara, P. Verma, R. Gupta, M. Yousuf, O.A. Trivedi, D. Mohanty, A. Tyagi, R. Sankaranarayanan, and R.S. Gokhale. 2009. “Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis.” Nat Chem Biol 5 (3):166-173. doi: 10.1038/nchembio.143.
  • Kaushik, S., D. Mohanty, and A. Surolia. 2009. “The role of metal ions in substrate recognition and stability of concanavalin A: a molecular dynamics study.” Biophys J 96 (1):21-34. doi: 10.1529/biophysj.108.134601.
  • Ansari, M.Z., J. Sharma, R.S. Gokhale, and D. Mohanty. 2008. “In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites.” BMC Bioinformatics 9:454. doi: 10.1186/1471-2105-9-454.
  • Chopra, T., S. Banerjee, S. Gupta, G. Yadav, S. Anand, A. Surolia, R.P. Roy, D. Mohanty, and R.S. Gokhale. 2008. “Novel intermolecular iterative mechanism for biosynthesis of mycoketide catalyzed by a bimodular polyketide synthase.” PLoS Biol 6 (7):e163. doi: 10.1371/journal.pbio.0060163.
  • Ghosh, R., A. Chhabra, P.A. Phatale, S.K. Samrat, J. Sharma, A. Gosain, D. Mohanty, S. Saran, and R.S. Gokhale. 2008. “Dissecting the functional role of polyketide synthases in Dictyostelium discoideum: biosynthesis of the differentiation regulating factor 4-methyl-5-pentylbenzene-1,3-diol.” J Biol Chem 283 (17):11348-11354. doi: 10.1074/jbc.M709588200.
  • Natarajan, V.T., D. Mohanty, and R.S. Gokhale. 2008. “Biosynthesis of mycobacterial lipids by multifunctional polyketide synthases.” The mycobacterial cell envelope:235-248.
  • Gokhale, R.S., R. Sankaranarayanan, and D. Mohanty. 2007. “Versatility of polyketide synthases in generating metabolic diversity.” Curr Opin Struct Biol 17 (6):736-743. doi: 10.1016/j.sbi.2007.08.021.
  • Kumar, N., and D. Mohanty. 2007. “MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes.” Nucleic Acids Res 35 (Web Server issue):W549-555. doi: 10.1093/nar/gkm266.
  • Goyal, K., D. Mohanty, and S.C. Mande. 2007. “PAR-3D: a server to predict protein active site residues.” Nucleic Acids Res 35 (Web Server issue):W503-505. doi: 10.1093/nar/gkm252.
  • Gokhale, R.S., P. Saxena, T. Chopra, and D. Mohanty. 2007. “Versatile polyketide enzymatic machinery for the biosynthesis of complex mycobacterial lipids.” Nat Prod Rep 24 (2):267-277. doi: 10.1039/b616817p.
  • Krithika, R., U. Marathe, P. Saxena, M.Z. Ansari, D. Mohanty, and R.S. Gokhale. 2006. “A genetic locus required for iron acquisition in Mycobacterium tuberculosis.” Proc Natl Acad Sci U S A 103 (7):2069-2074. doi: 10.1073/pnas.0507924103.
  • Arora, P., A. Vats, P. Saxena, D. Mohanty, and R.S. Gokhale. 2005. “Promiscuous fatty acyl CoA ligases produce acyl-CoA and acyl-SNAC precursors for polyketide biosynthesis.” J Am Chem Soc 127 (26):9388-9389. doi: 10.1021/ja052991s.
  • Kamra, P., R.S. Gokhale, and D. Mohanty. 2005. “SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites.” Nucleic Acids Res 33 (Web Server issue):W220-225. doi: 10.1093/nar/gki449.
  • Trivedi, O.A., P. Arora, A. Vats, M.Z. Ansari, R. Tickoo, V. Sridharan, D. Mohanty, and R.S. Gokhale. 2005. “Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid.” Mol Cell 17 (5):631-643. doi: 10.1016/j.molcel.2005.02.009.
  • Ansari, M.Z., G. Yadav, R.S. Gokhale, and D. Mohanty. 2004. “NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases.” Nucleic Acids Res 32 (Web Server issue):W405-413. doi: 10.1093/nar/gkh359.
  • Trivedi, O.A., P. Arora, V. Sridharan, R. Tickoo, D. Mohanty, and R.S. Gokhale. 2004. “Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria.” Nature 428 (6981):441-445. doi: 10.1038/nature02384.
  • Trivedi, O.A., P. Arora, V. Sridharan, R. Tickoo, D. Mohanty, and R.S. Gokhale. 2004. “Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria.” Nature 428 (6981):441-445. doi: 10.1038/nature02384.
  • Saxena, P., G. Yadav, D. Mohanty, and R.S. Gokhale. 2003. “A new family of type III polyketide synthases in Mycobacterium tuberculosis.” J Biol Chem 278 (45):44780-44790. doi: 10.1074/jbc.M306714200.
  • Yadav, G., R.S. Gokhale, and D. Mohanty. 2003. “SEARCHPKS: A program for detection and analysis of polyketide synthase domains.” Nucleic Acids Res 31 (13):3654-3658. doi: 10.1093/nar/gkg607.
  • Yadav, G., R.S. Gokhale, and D. Mohanty. 2003. “Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases.” J Mol Biol 328 (2):335-363. doi: 10.1016/s0022-2836(03)00232-8.
  • Mohanty, D., R. Elber, and D. Thirumalai. 2000. “Probing the role of local propensity in peptide turn formation.” International Journal of Quantum Chemistry 80 (4‐5):1125-1128.
  • Mohanty, D., A. Kolinski, and J. Skolnick. 1999. “De novo simulations of the folding thermodynamics of the GCN4 leucine zipper.” Biophys J 77 (1):54-69. doi: 10.1016/S0006-3495(99)76872-4.
  • Mohanty, D., B.N. Dominy, A. Kolinski, C.L. Brooks III, and J. Skolnick. 1999. “Correlation between knowledge‐based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper.” Proteins: Structure, Function, and Bioinformatics 35 (4):447-452.
  • Skolnick, J., A. Kolinski, and D. Mohanty. 1999. “De novo predictions of the quaternary structure of leucine zippers and other coiled coils.” International Journal of Quantum Chemistry 75 (3):165-176.
  • Elber, R., D. Mohanty, and C. Simmerling. 1998. “Dynamics of peptide folding.” In Classical And Quantum Dynamics In Condensed Phase Simulations, 423-444. World Scientific.
  • Mohanty, D., R. Elber, D. Thirumalai, D. Beglov, and B. Roux. 1997. “Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water.” J Mol Biol 272 (3):423-442. doi: 10.1006/jmbi.1997.1246.
  • Mohanty, D., and M. Bansal. 1995. “Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study.” Biophys J 69 (3):1046-1067. doi: 10.1016/S0006-3495(95)79979-9.
  • Mohanty, D., and M. Bansal. 1994. “Conformational polymorphism in telomeric structures: loop orientation and interloop pairing in d(G4TnG4).” Biopolymers 34 (9):1187-1211. doi: 10.1002/bip.360340908.
  • Mohanty, D., and M. Bansal. 1993. “Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover.” Nucleic Acids Res 21 (8):1767-1774. doi: 10.1093/nar/21.8.1767.
  • Balagurumoorthy, P., S.K. Brahmachari, D. Mohanty, M. Bansal, and V. Sasisekharan. 1992. “Hairpin and parallel quartet structures for telomeric sequences.” Nucleic Acids Res 20 (15):4061-4067. doi: 10.1093/nar/20.15.4061.
  • Mohanty, D., and M. Bansal. 1991. “DNA polymorphism and local variation in base-pair orientation: a theoretical rationale.” J Biomol Struct Dyn 9 (1):127-142. doi: 10.1080/07391102.1991.10507898.