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…
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…
Abdallah A. Mohamed, Seychelle M. Vos
Cyclin-dependent kinases (CDK) dynamically regulate RNA Polymerase (Pol) II during each stage of transcription. Phosphorylation of RNA Pol II and associated transcription factors by CDKs enables stage-specific exchange of factors. CDK9 and a cyclin partner (CYCT1, T2 or K) comprise the Positive Transcription Elongation…
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…
Minha Park, Shinwoo Kim, Seokhyun Moon, Hyeongwoo Kim + 2 more
Co-folding models accurately predict biomolecular complexes, but how their internal representations support joint structure prediction remains unclear. We analyze the Boltz-1 trunk by decomposing its pair representation into intra-chain and inter-chain blocks and applying ablation, layer-wise representation geometry…
Alexander Aichmair, Heiko Graichen, Nimrod Snir, Benjamin V. Bloch + 4 more
Total knee arthroplasty (TKA) is a highly successful procedure for the treatment of end-stage osteoarthritis of the knee . While mechanical alignment has been considered the gold standard for decades , personalized alignment strategies have been established with the aim of improving postoperative patient satisfaction…
Mitsuhiko Kubo, Kazuhiro Uenaka, Hitomi Fujikawa, Tsutomu Maeda + 4 more
High tibial osteotomy (HTO) is an established procedure for the treatment of knee disorders associated with coronal malalignment. Based on deformity analysis, HTO is performed to correct pathological lower-limb alignment and optimize load distribution across the knee joint. In patients with medial compartmental knee…
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…
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…
Sake Salverda, Ernst van der Wal, Thomas Toet, Mischa Hoogeman + 1 more
Figure [mp70671-fig-0006] shows flatness versus central 80% field width for both the nominal alignment and a misaligned measurement ( rotation, translation) for several CTC distances. Increasing the number of minibeams increases the central 80% field width. For both SSCs and MSCs, a minimum field width is required to…
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…
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…