@article {163998, title = {Cascade PSI-BLAST 2.0: a fast-searching parallelized remote homology detection tool and development of Cascade web server 2.0}, journal = {Springer Nature Link}, year = {2026}, month = {18 February 2026}, abstract = {

Remote homology detection is critical for inferring evolutionary and functional relationships among proteins, but divergence below 30\% identity often hinders standard sequence-based searches. Profile-based methods and HMMs improve sensitivity, yet many distant homologues remain undetected. Cascade PSI-BLAST uses efficient, iterative, multi-generation searches of intermediate hits to bridge sequence gaps, constructing successive PSSMs that reveal remote relationships without structural information. However, its application to ultra-large databases such as NR and UniProt is computationally intensive. We address this limitation by optimizing intermediate selection and enabling distributed execution across multiple CPUs or servers, significantly enhancing throughput and resource utilization while preserving detection sensitivity.

}, keywords = {Cascade PSI_BLAST, GNU parallel, Parallel processing, PSI BLAST, Remote homology search, Webserver}, doi = {https://doi.org/10.1186/s12859-026-06366-7 }, url = {https://link.springer.com/article/10.1186/s12859-026-06366-7}, author = {Soumya Nayak and Dheemanth Reddy Regati and Murugavel Pavalam and R. Sowdhamini} } @article {158502, title = {Computational exploration of Arabidopsis thaliana N-Myc downregulated-like-1 for protein{\textendash}protein interaction and phylogenetic conservation}, year = {2025}, abstract = {

N-Myc downregulated-like (NDL) proteins belong to the α/β-hydrolase-fold-containing protein family. NDLs are interacting partners of G-protein subunits which are involved in abiotic and biotic stress signaling mechanisms in plants. Three NDLs (NDL1, NDL2, and NDL3) have been identified in\ Arabidopsis thaliana. The NDL1 interactome reveals its interaction with numerous proteins involved in diverse plant functions, suggesting its role in various signaling mechanisms. The current study was designed to explore the level of conservation of NDL proteins across the plant kingdom to analyze protein structure for the conserved sites involved in protein{\textendash}protein interactions. We analyzed NDL proteins from different plant groups for sequence conservation patterns through phylogenetic and motif analyses. Subsequently, homology-based models were built for NDLs and their selected interactors using MODELLER, and interaction sites were also analyzed using molecular docking. Overall, our study revealed sequence conservation within the NDL family and the presence of several conserved motifs across diverse plant groups. Additionally, docking analysis suggests that two specific regions, spanning positions 40{\textendash}50 and 135{\textendash}170 in the NDL1 structure, may serve as hotspots for various protein{\textendash}protein interactions.

}, doi = {10.1007/s12038-025-00520-8 }, url = {https://link.springer.com/article/10.1007/s12038-025-00520-8}, author = {Abhishek Kanojia and Asani Bhaduri and Soumya Nayak and R Sowdhamini and Yashwanti Mudgil} }