9,183 results found
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Structure-based prediction of T cell receptor:peptide-MHC interactions

    Philip Bradley
    The AlphaFold protein structure prediction network can be specialized for T cell receptor docking, leading to improved models of ternary complexes and some ability to discriminate correct from incorrect peptide epitopes.
    1. Structural Biology and Molecular Biophysics
    2. Evolutionary Biology

    Large-scale determination of previously unsolved protein structures using evolutionary information

    Sergey Ovchinnikov, Lisa Kinch ... David Baker
    A new method of protein structure prediction that incorporates residue–residue co-evolution information into the Rosetta structure prediction program was used to develop models for 58 large protein families that had no previous structural information.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    Pi-Pi contacts are an overlooked protein feature relevant to phase separation

    Robert McCoy Vernon, Paul Andrew Chong ... Julie Deborah Forman-Kay
    Statistics on the frequencies of pi interactions in folded protein structures enable successful prediction of intrinsically disordered protein phase separation, with clear implications for a physical understanding of cellular organization.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing

    Jayashree Kumar, Lela Lackey ... Alain Laederach
    A novel model is presented that reconciles in-cell structure probing data with splicing regulatory elements to predict exon 10 inclusion of the Tau gene with high accuracy for 53 splice altering mutations.
    1. Evolutionary Biology

    Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

    Sergey Ovchinnikov, Hetunandan Kamisetty, David Baker
    Co-evolving residue pairs in the different components of a protein complex almost always make contact across the protein–protein interface, thus providing powerful restraints for the modeling of protein complexes.
    1. Structural Biology and Molecular Biophysics

    Sampling alternative conformational states of transporters and receptors with AlphaFold2

    Diego del Alamo, Davide Sala ... Jens Meiler
    Alternative conformations of membrane protein structures can be predicted to high accuracy with AlphaFold2 by reducing the depth of the multiple sequence alignments used for modeling.
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    1. Structural Biology and Molecular Biophysics

    Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis

    Anusmita Sahoo, Shruti Khare ... Raghavan Varadarajan
    Experimental determination of residue contacts from mutational data allows model discrimination and identification of in vivo functional conformations of proteins.
    1. Computational and Systems Biology

    Genome-scale annotation of protein binding sites via language model and geometric deep learning

    Qianmu Yuan, Chong Tian, Yuedong Yang
    Integration of language model and geometric deep learning enables accurate and efficient genome-scale annotation of comprehensive protein-ligand binding sites.
    1. Neuroscience

    The neural basis of intelligence in fine-grained cortical topographies

    Ma Feilong, J Swaroop Guntupalli, James V Haxby
    Individual differences in intelligence are based on information processing that is embedded in fine-scale structure in cortical systems for self-generated thought, which was revealed by resolving topographic idiosyncrasies with hyperalignment.
    1. Genetics and Genomics
    2. Structural Biology and Molecular Biophysics

    Structure-guided isoform identification for the human transcriptome

    Markus J Sommer, Sooyoung Cha ... Steven L Salzberg
    The ability to accurately predict a protein's structure gives us an entirely new way to annotate the human genome.

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