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Preprint . 2023
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Article . 2024
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Proteins Structure Function and Bioinformatics
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Article . 2023 . Peer-reviewed
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Invariant point message passing for protein side chain packing

Authors: Nicholas Z. Randolph; Brian Kuhlman;

Invariant point message passing for protein side chain packing

Abstract

Abstract Protein side chain packing (PSCP) is a fundamental problem in the field of protein engineering, as high‐confidence and low‐energy conformations of amino acid side chains are crucial for understanding (and designing) protein folding, protein–protein interactions, and protein‐ligand interactions. Traditional PSCP methods (such as the Rosetta Packer) often rely on a library of discrete side chain conformations, or rotamers, and a forcefield to guide the structure to low‐energy conformations. Recently, deep learning (DL) based methods (such as DLPacker, AttnPacker, and DiffPack) have demonstrated state‐of‐the‐art predictions and speed in the PSCP task. Building off the success of geometric graph neural networks for protein modeling, we present the Protein Invariant Point Packer (PIPPack) which effectively processes local structural and sequence information to produce realistic, idealized side chain coordinates using ‐angle distribution predictions and geometry‐aware invariant point message passing (IPMP). On a test set of ∼1400 high‐quality protein chains, PIPPack is highly competitive with other state‐of‐the‐art PSCP methods in rotamer recovery and per‐residue RMSD but is significantly faster.

Keywords

Models, Molecular, Protein Folding, Protein Conformation, Proteins, Computational Biology, Protein Engineering, Article, Deep Learning, Neural Networks, Computer, Amino Acids, Databases, Protein, Software, Algorithms

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    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    9
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
9
Top 10%
Average
Top 10%
Green