Path collective variables reduce a high-dimensional transition to a progress coordinate, s, and an orthogonal distance, z. Computing the free energy along s often requires restraining z, so that sampling embraces a tube centered on the reference path. However, a conventional fixed half-harmonic wall demands an a priori...
Radu A. Talmazan, Cheng Giuseppe Chen, Chenyu Tang et al.· The Journal of Chemical Phys...· 0 citations
Delay is an inherent feature of genetic regulatory networks. It represents the time required for the assembly of functional regulator proteins. The protein production process is complex, as it includes transcription, translocation, translation, folding, and oligomerization. Because these steps are noisy, the resulting...
Sean Campbell, Courtney C. White, Amanda M. Alexander et al.· SIAM Journal on Life Science...· 0 citations
Sequence differences between deposited macromolecular models and their UniProt references are recorded in the mmCIF category _struct_ref_seq_dif, and intentional substitutions are expected to populate _entity_poly.pdbx_mutation, the field that structured queries read. When a substitution is not declared, the difference...
Michael T. Varman· Zenodo (CERN European Organi...· 0 citations
Cyclic oligonucleotide-based antiphage signaling systems (CBASS) protect bacteria from bacteriophage infection by producing cyclic nucleotide second messengers that activate downstream effector proteins. Cyclic guanosine monophosphate-adenosine monophosphate (cGAMP)-activated phospholipase in Vibrio (CapV) is a prevale...
Samson Marvellous Oladeji, Shay Adio, C. Vennard et al.· ACS Chemical Biology· 0 citations
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Ultrasonography (USG) is central to the diagnosis of pediatric appendicitis, but operator dependency and limited access can delay triage. This study aimed to develop an explainable machine learning model that estimates the USG-assisted clinical diagnosis of appendicitis from pre-imaging clinical and laboratory data alo...
Hilal Yumrutaş, Selahaddin Batuhan Akben, Yavuz Selim İşler· Bratislavské lekárske list...· 0 citations
It is reported that PML-1 itself harbors a previously structurally uncharacterized nucleic acid-binding domain, termed PXL, which is unique to isoform 1 and specifically binds G-rich oligonucleotides implicated in G-quadruplex formation and displays a strong in vitro preference for polyUG RNA.
Daniel Fairchild, Irina V. Semenova, Dane H. Geddes-Buehre et al.· Nucleic Acids Research· 0 citations
This work defines a previously unrecognized class of oncogenic fusions that preserve protein structure but replace the 5' untranslated region (5' UTR), thereby rewiring translational regulation in cancer patients.
M. Cerqua, Estelle Bigot, Cédric Chaveroux et al.· Cell Reports· 0 citations
This review underscores the potential of BamA as a next-generation antibacterial target and outlines future directions for the development of effective therapeutics against multidrug-resistant Gram-negative bacteria.
A. Al-Karmalawy, A. A. Al Khatib, S. Hawas· RSC Advances· 0 citations
In six cancer proteomics cohorts, 334 small-protein candidates were identified, including 36 differentially expressed small proteins (DESPs) exhibiting strong cancer-type specificity, suggesting specialized functional roles in tumor biology and underscore the potential of SPROTify as a robust, protein-centric engine fo...
Chien-Han Yuan, Pei-Wen Wu, Ing-Luen Shyu et al.· New Biotechnology· 0 citations
Resolving cancer-associated protein variants remains difficult when variants share similar molecular masses and folded structures. Conventional assays often require labels or provide ensemble-averaged readouts, limiting their ability to resolve subtle variant differences. Here, a YaxAB nanopore workflow is presented fo...
Min-Ji Chung, Sohee Oh, Jin-Sik Kim et al.· Small Methods· 0 citations
Large language models are increasingly competent at leveraging scientific knowledge and existing computational tools to execute complex workflows. At present, little information exists on their ability to reconstruct tools when given limited descriptions of such tools. We introduce an evaluation titled ReproBAIT (Repro...
Shiv Muthupandiyan, T. H. Dur, Macey Walker et al.· 0 citations
Background: Current cancer initiation models, including multi-hit genomic models and chromosomal instability (CIN) frameworks, do not account for a mechanistically distinct upstream event: progressive protein coupling failure at the spindle pole during mitosis. We propose a novel hypothesis in which coupling failure am...
Stoffel Brandy· Zenodo (CERN European Organi...· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
