12 papers · ranked by Valyu relevance
Xuebin Feng, Emma R. Master
Sequence similarity networks (SSNs) are graphical representations of sequence relationship frequently used for exploring protein sequence space. Conventional SSN workflows typically use BLAST to calculate sequence similarities and rely on external visualization tools to generate the final networks. Consequently, raw…
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…
ChenTianyi Yang, Andrew Thwaites, Cai Wingfield, Chao Zhang + 1 more
The brain builds meaning from speech in stages, transforming acoustic input into linguistic comprehension. Yet where comprehension separates from general acoustic processing has been difficult to localize, because the two are tightly entangled in continuous speech. Here we align the activity of 145,000 individual…
Julie Boisard, Shelby K Williams, Andrew J Roger, Courtney W Stairs
Mitochondrial proteome reconstruction from eukaryotic sequence data typically relies on prediction of mitochondrial targeting signals (MTSs). However, MTS predictors are primarily trained on model organisms and may perform poorly in phylogenetically divergent lineages or in organisms with atypical or reduced targeting…
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…
Eliezer Masliah
How transient neural representations become integrated and stable enough to function as internal neural models remains incompletely understood. Grounded in efficient coding, Bayesian and predictive frameworks, recurrent and attractor dynamics, neural state-space models, and systems neuroscience, the Principle of…
Sake Salverda, Ernst van der Wal, Thomas Toet, Mischa Hoogeman + 1 more
4## DISCUSSION In this study we developed a setup to accurately measure the lateral profile of a proton minibeam. The setup, based on the microDiamond detector and automated positioning, substantially reduces measurement time compared to conventional film dosimetry. The setup takes about 10 minutes and can measure a…
Sara Otaegi-Ugartemendia, Gabriela N. Condezo, Marta Martínez, Panos G. Kalatzis + 3 more
Non-tailed phages remain underexplored in marine environments, as tailed phages have long dominated sequence and culture collections. Yet recent surveys suggest that non-tailed phages may be more abundant and have distinct impacts on microbial mortality and gene transfer. Here, we solve the structure of Vibrio…
Fabio Cumbo, Kabir Dhillon, M. Hassan Najafi, Sercan Aygun + 1 more
The exponential growth of genomic databases necessitates alignment-free methods for comparing genomes. While MinHash-based tools have revolutionized this field by efficiently estimating the Average Nucleotide Identity based on k-mer sets, they inherently discard structural genomic information. We introduce HyperSketch…
Alp Tartici, Mihajlo Stojkovic, Anru Tian, Michael C. Jewett + 2 more
Protein engineering has important implications in the bioeconomy, enabling applications in materials, medicine, and energy. A key challenge is designing protein sequences that have a specific form and function. Protein inverse folding seeks to address this challenge by identifying amino acid sequences compatible with a…
Davi Nakajima An, Amy L. Schaefer, Szu-Min Chang, Bianxia Bai + 4 more
Acyl-homoserine lactone (AHL) quorum sensing enables many species of proteobacteria to coordinate collective behaviors. In such systems, a synthase produces an AHL signal, which is sensed by a LuxR-family receptor. Despite extensive genomic annotation of LuxR homologs, preferred AHLs for most receptors remain unknown…