Computational approaches to structure, function, and evolution of biological molecules.
Research Areas
We perform in silico analysis of domain architecture, protein-protein interactions, and sequence motifs across diverse protein families. Projects have included structural analysis of human NEK10, SPD-2, and knottin-containing venom proteins.
Computational analysis of venom peptides and extracellular vesicle cargo from parasitoid wasps (Drosophila parasitoids, Leptopilina). We use structural and sequence analysis to characterize toxin-related proteins and predict their mechanisms of action.
We model and characterize protein domain families at the genome-wide scale. Recent work includes a comprehensive study of Pleckstrin Homology (PH) domains in Chlamydomonas reinhardtii and ciliary kinase domains in C. elegans.
Using large-scale and long-time all-atom molecular dynamics simulations to study how amphipathic peptides aggregate into amyloid-like fibrils, with implications for understanding protein misfolding diseases.
Publications
Chou J, Li MZ, Wey B, Mumtaz M, Ramroop JR, Singh S, Govind S. Venomous Cargo: Diverse Toxin-Related Proteins Are Associated with Extracellular Vesicles in Parasitoid Wasp Venom. Pathogens. 2025 Mar 5;14(3).
doi: 10.3390/pathogens14030255 · PubMed: 40137740Aksoy M, Krupitskaya M, Singh SM. A Genome-Wide Modeling and Characterization Study of Pleckstrin Homology Domains in Chlamydomonas reinhardtii. Plants (Basel). 2025 Aug 22;14(17).
doi: 10.3390/plants14172607 · PubMed: 40941772Eichner AS, Zimmerman N, San A, Singh S. In Silico Analysis of Human NEK10 Reveals Novel Domain Architecture and Protein-Protein Interactions. Proteins. 2025 Oct 3. [Epub ahead of print]
doi: 10.1002/prot.70067 · PubMed: 41044802Guest editor of Special Issue "Computational Approaches in Mechanisms of Pathogenesis" for the open-access MDPI journal Pathogens, 2025.
Power KM, Nguyen KC, Silva A, Singh S, Hall DH, Rongo C, Barr MM. NEKL-4 regulates microtubule stability and mitochondrial health in ciliated neurons. J Cell Biol. 2024 Sep 2;223(9).
doi: 10.1083/jcb.202402006 · PubMed: 38767515Arguelles J, Lee J, Cardenas LV, Govind S, Singh S. In Silico Analysis of a Drosophila Parasitoid Venom Peptide Reveals Prevalence of the Cation-Polar-Cation Clip Motif in Knottin Proteins. Pathogens 2023, 12, 143.
doi: 10.3390/pathogens12010143Jalali S, Yang Y, Mahmoudinobar F, Singh SM, Nilsson B, Dias C. Using large-scale and long-time all-atom simulations to study the aggregation of amphipathic peptides into amyloid-like fibrils. Journal of Molecular Liquids 347, 118283.
Murph M, Singh S, Schvarzstein M. The Centrosomal Swiss Army Knife: A combined in silico and in vivo approach to the structure-function annotation of SPD-2 provides mechanistic insight into its functional diversity. Cell Cycle (In press; preprint available from bioRxiv 2021.04.22.441031).