5 papers · ranked by Valyu relevance
Yiming Xue, Xiaojian Liu, Weimin Zhu, Shengfan Wang + 2 more
While protein-RNA interactions are fundamental to post-transcriptional processes, achieving a holistic understanding of their regulatory logic remains challenging. Current computational models often treat binding affinity, interface mapping, and RNA design as isolated tasks, thereby failing to provide a unified…
Kapali Suri, Anshul Yadav, Abhishek Tripathi, N. Arul Murugan
Protein-ligand pose prediction is central to structure-based drug discovery, yet the relative performance of physics-based and AI-driven methods under realistic cross-docking conditions remains insufficiently characterized. Here, we compare physics-based docking methods (AutoDock4, AutoDock Vina, and DOCK 6) with…
Ana Lúcia Leitão, Francisco J Enguita
The evolution of molecular visualization software represents a pivotal yet often underappreciated dimension of computational structural biology and bioinformatics. As the scale and complexity of structural datasets increase, spanning from cryo-electron microscopy reconstructions to proteome-wide AI-predicted models…
Yusuke Tsuruta, Hirotaka Inoue, Kenta Hagiwara, Charles S Hoffman + 1 more
An appropriate transcriptional response to external stresses is crucial for all organisms. Gene expression is regulated by transcription factors (TFs) binding to specific DNA cis-elements. However, how individual TFs achieve stress-specific binding remains elusive. Here we examine the molecular basis of the…
Manasi Bora, Prokriti Paul, Sanchaita Rajkhowa, Harshita Sonar + 4 more
The rapid rise of multidrug-resistant (MDR) Klebsiella pneumoniae has created a major global health challenge due to the limited availability of conserved therapeutic targets effective across diverse resistant strains. In this study, an integrative computational target-discovery and drug-repurposing framework was…