Detection of hydrogen-bond signature patterns in protein families. - Tejasvini Prasad; M. N. Prathima; Nagasuma Chandra (Bioinform., 2003)

Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs. - Karthik Raman 002; Preethi Rajagopalan; Nagasuma R. Chandra (PLoS Comput. Biol., 2005)

Projections for fast protein structure retrieval. - Sourangshu Bhattacharya; Chiranjib Bhattacharyya; Nagasuma R. Chandra (BMC Bioinform., 2006)

Structural alignment based kernels for protein structure classification. - Sourangshu Bhattacharya; Chiranjib Bhattacharyya; Nagasuma R. Chandra (ICML, 2007)

Comparison of protein structures by growing neighborhood alignments. - Sourangshu Bhattacharya; Chiranjib Bhattacharyya; Nagasuma R. Chandra (BMC Bioinform., 2007)

PocketMatch: A new algorithm to compare binding sites in protein structures. - Kalidas Yeturu; Nagasuma R. Chandra (BMC Bioinform., 2008)

targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. - Karthik Raman 002; Kalidas Yeturu; Nagasuma R. Chandra (BMC Syst. Biol., 2008)

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data. - Sahely Bhadra; Chiranjib Bhattacharyya; Nagasuma R. Chandra; I. Saira Mian (Algorithms Mol. Biol., 2009)

Flux balance analysis of biological systems: applications and challenges. - Karthik Raman 002; Nagasuma R. Chandra (Briefings Bioinform., 2009)

Enhanced flux balance analysis to model metabolic networks. - Nishanth Ulhas Nair; Navin Goyal; Nagasuma R. Chandra (BCB, 2010)

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules. - Kalidas Yeturu; Tapani Utriainen; Graham J. L. Kemp; Nagasuma R. Chandra (BMC Bioinform., 2010)

PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures. - Kalidas Yeturu; Nagasuma R. Chandra (J. Chem. Inf. Model., 2011)

Virtual screening, identification and experimental testing of novel inhibitors of PBEF1/Visfatin/NMPRTase for glioma therapy. - Nagasuma Chandra; Raghu Bhagavat; Eshita Sharma; P. Sreekanthreddy; Kumaravel Somasundaram (J. Clin. Bioinform., 2011)

PocketAnnotate: towards site-based function annotation. - Praveen Anand; Kalidas Yeturu; Nagasuma R. Chandra (Nucleic Acids Res., 2012)

A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis. - Soma Ghosh; Priyanka Baloni; Sumanta Mukherjee; Praveen Anand; Nagasuma R. Chandra (BMC Syst. Biol., 2013)

Current trends in modeling host-pathogen interactions. - Sumanta Mukherjee; Awanti Sambarey; Karyala Prashanthi; Nagasuma R. Chandra (WIREs Data Mining Knowl. Discov., 2013)

Different cancer cell lines resistant to the same drug exhibit differences in folate pathway dynamics. - Amrisha Bhosle; Nagasuma Chandra (BIBM, 2014)

PLIC: protein-ligand interaction clusters. - Praveen Anand; Deepesh Nagarajan; Sumanta Mukherjee; Nagasuma R. Chandra (Database J. Biol. Databases Curation, 2014)

EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks. - Narmada Sambaturu; Madhulika Mishra; Nagasuma Chandra (BIBM, 2015)

SInCRe - structural interactome computational resource for Mycobacterium tuberculosis. - Rahul Metri; Sridhar Hariharaputran; Gayatri Ramakrishnan; Praveen Anand; Upadhyayula S. Raghavender; Bernardo Ochoa-Montaño; Alicia P. Higueruelo; Ramanathan Sowdhamini; Nagasuma R. Chandra; Tom L. Blundell; Narayanaswamy Srinivasan (Database J. Biol. Databases Curation, 2015)

CHEXVIS: a tool for molecular channel extraction and visualization. - Talha Bin Masood; Sankaran Sandhya; Nagasuma R. Chandra; Vijay Natarajan (BMC Bioinform., 2015)

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. - Richa Mudgal; Sankaran Sandhya; Gayatri Kumar; Ramanathan Sowdhamini; Nagasuma R. Chandra; Narayanaswamy Srinivasan (Nucleic Acids Res., 2015)

Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study. - Soma Ghosh; Nagasuma R. Chandra; Saraswathi Vishveshwara (PLoS Comput. Biol., 2015)

HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials. - Sumanta Mukherjee; Chiranjib Bhattacharyya; Nagasuma Chandra (Bioinform., 2016)

MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature. - Nithin Shivashankar; Sonali Patil; Amrisha Bhosle; Nagasuma Chandra; Vijay Natarajan (BMC Bioinform., 2016)

Probing the Druggability Limits for Enzymes of the NAD Biosynthetic Network in Glioma. - Jyothi Padiadpu; Madhulika Mishra; Eshita Sharma; Uchurappa Mala; Kumar Somasundaram; Nagasuma Chandra (J. Chem. Inf. Model., 2016)

Modelling metabolic rewiring during melanoma progression using flux balance analysis. - Rahul Metri; Shikhar Saxena; Madhulika Mishra; Nagasuma Chandra (BIBM, 2017)

Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza. - Narmada Sambaturu; Sumanta Mukherjee; Martín López-García; Carmen Molina-París; Gautam I. Menon; Nagasuma Chandra (PLoS Comput. Biol., 2018)

A Uniform In Vitro Efficacy Dataset to Guide Antimicrobial Peptide Design. - Deepesh Nagarajan; Tushar Nagarajan; Neha Nanajkar; Nagasuma Chandra (Data, 2019)

PathExt: a general framework for path-based mining of omics-integrated biological networks. - Narmada Sambaturu; Vaidehi Pusadkar; Sridhar Hannenhalli; Nagasuma Chandra (Bioinform., 2021)

Fast Local Alignment of Protein Pockets (FLAPP): A System-Compiled Program for Large-Scale Binding Site Alignment. - Santhosh Sankar; Naren Chandran Sakthivel; Nagasuma Chandra (J. Chem. Inf. Model., 2022)

SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites. - Santhosh Sankar; Nagasuma Chandra (PLoS Comput. Biol., 2022)

PathTracer Comprehensively Identifies Hypoxia-Induced Dormancy Adaptations in Mycobacterium tuberculosis. - Ushashi Banerjee; Adithya Chedere; Raksha Padaki; Abhilash Mohan; Narmada Sambaturu; Amit Singh; Nagasuma Chandra (J. Chem. Inf. Model., 2023)