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  1. Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike

    Publication
    Omicron BA.1 is a highly infectious variant of SARS-CoV-2 that carries more than thirty mutations on the spike protein in comparison to the Wuhan wild …

  2. Catching actin proteins in action

    Publication
    Two groups have visualized actin — the protein polymer that gives cells their shape — at high resolution. The structures provide in-depth views of the polymer as it adopts …

  3. Protocol for iterative optimization of modified peptides bound to protein targets

    Publication
    Peptides are commonly used as therapeutic agents. However, they suffer from easy degradation and instability. Replacing natural by non-natural amino acids can avoid these problems, and potentially …

  4. Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations

    Publication
    Simulations with adaptive time-dependent bias enable an efficient exploration of the conformational space of a system. However, the dynamic information is altered by the bias. Infrequent metadynamics …

  5. Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol

    Publication
    Epitopes that bind simultaneously to all human alleles of Major Histocompatibility Complex class II (MHC II) are considered one of the key factors for the development of improved …

  6. Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models

    Publication
    Abstract Several antimicrobial peptides, including magainin and the human cathelicidin LL-37, act by forming pores in bacterial membranes. Bacteria such as Staphylococcus aureus modify their membrane's …

  7. Application of ensemble pharmacophore-based virtual screening to the discovery of novel antimitotic tubulin inhibitors

    Publication
    Tubulin is a well-validated target for herbicides, fungicides, anti-parasitic, and anti-tumor drugs. Many of the non-cancer tubulin drugs bind to its colchicine site but …

  8. A Bayesian approach for extracting free energy profiles from cryo-electron microscopy experiments using a path collective variable

    Publication
    Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single-particle nature …