• Protein oligomer structure prediction using GALAXY in CASP14

    13 days ago - By Wiley

    Abstract
    Proteins perform their functions by interacting with other biomolecules. For these interactions, proteins often form homo- or hetero-oligomers as well. Thus, oligomer protein structures provide important clues regarding the biological roles of proteins. To this end, computational prediction of oligomer structures may be a useful tool in the absence of experimentally resolved structures. Here, we describe our server and human-expert methods used to predict oligomer structures in the CASP14 experiment. Examples are provided for cases in which manual domain-splitting led to improved...
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  • Protein structure prediction using deep learning distance and hydrogen‐bonding restraints in CASP14

    13 days ago - By Wiley

    Abstract
    In this article, we report 3D structure prediction results by two of our best server groups in CASP14. These two servers were built based on the D-I-TASSER and D-QUARK algorithms, which integrated four newly developed components into the classical protein folding pipelines, I-TASSER and QUARK, respectively. The new components include: a new multiple sequence alignment collection tool, DeepMSA2, which is extended from the DeepMSA program; a contact-based domain boundary prediction algorithm, FUpred, to detect protein domain boundaries; a residual convolutional neural network-based...
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