SEARCHPKS: a program for detection and analysis of polyketide synthase domains. - Gitanjali Yadav; Rajesh S. Gokhale; Debasisa Mohanty (Nucleic Acids Res., 2003)

NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. - Mohd. Zeeshan Ansari; Gitanjali Yadav; Rajesh S. Gokhale; Debasisa Mohanty (Nucleic Acids Res., 2004)

SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites. - Pankaj Kamra; Rajesh S. Gokhale; Debasisa Mohanty (Nucleic Acids Res., 2005)

PAR-3D: a server to predict protein active site residues. - Kshama Goyal; Debasisa Mohanty; Shekhar C. Mande (Nucleic Acids Res., 2007)

MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. - Narendra Kumar; Debasisa Mohanty (Nucleic Acids Res., 2007)

In silico analysis of methyltransferase domains involved in biosynthesis of secondary metabolites. - Mohd. Zeeshan Ansari; Jyoti Sharma; Rajesh S. Gokhale; Debasisa Mohanty (BMC Bioinform., 2008)

RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways. - Deepak Sharma; Debasisa Mohanty; Avadhesha Surolia (Nucleic Acids Res., 2009)

Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis. - Gitanjali Yadav; Rajesh S. Gokhale; Debasisa Mohanty (PLoS Comput. Biol., 2009)

Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials. - Narendra Kumar; Debasisa Mohanty (Bioinform., 2010)

Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles. - Pankaj Khurana; Rajesh S. Gokhale; Debasisa Mohanty (BMC Bioinform., 2010)

SBSPKS: structure based sequence analysis of polyketide synthases. - Swadha Anand; M. V. R. Prasad; Gitanjali Yadav; Narendra Kumar; Jyoti Shehara; Mohd. Zeeshan Ansari; Debasisa Mohanty (Nucleic Acids Res., 2010)

Computational Methods for Identification of Novel Secondary Metabolite Biosynthetic Pathways by Genome Analysis. - Swadha Anand; Debasisa Mohanty (Handbook of Research on Computational and Systems Biology, 2011)

Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network. - Nikhil Prakash Damle; Debasisa Mohanty (Bioinform., 2014)

Structure-Based Multiscale Approach for Identification of Interaction Partners of PDZ Domains. - Garima Tiwari; Debasisa Mohanty (J. Chem. Inf. Model., 2014)

novPTMenzy: a database for enzymes involved in novel post-translational modifications. - Shradha Khater; Debasisa Mohanty (Database J. Biol. Databases Curation, 2015)

RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links. - Priyesh Agrawal; Shradha Khater; Money Gupta; Neetu Sain; Debasisa Mohanty (Nucleic Acids Res., 2017)

SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases. - Shradha Khater; Money Gupta; Priyesh Agrawal; Neetu Sain; Jyoti Prava; Priya Gupta; Mansi Grover; Narendra Kumar; Debasisa Mohanty (Nucleic Acids Res., 2017)

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. - Priya Gupta; Debasisa Mohanty (Briefings Bioinform., 2021)

A machine learning-based method for prediction of macrocyclization patterns of polyketides and non-ribosomal peptides. - Priyesh Agrawal; Debasisa Mohanty (Bioinform., 2021)

Pf-Phospho: a machine learning-based phosphorylation sites prediction tool for Plasmodium proteins. - Priya Gupta; Sureshkumar Venkadesan; Debasisa Mohanty (Briefings Bioinform., 2022)

ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes. - Akshay Khanduja; Manish Kumar; Debasisa Mohanty (Briefings Bioinform., 2023)

HgutMgene-Miner: In silico genome mining tool for deciphering the drug-metabolizing potential of human gut microbiome. - Sana Amir; Manish Kumar; Vikas Kumar; Debasisa Mohanty (Comput. Biol. Medicine, 2025)