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Protein Folding

Protein Folding

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

Conservation of Protein Domains

Conservation of Protein Domains

Protein Diffusion in the Membrane

Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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Related Experiment Video

Updated: Jul 6, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Invariant point message passing for protein side chain packing.

Nicholas Z Randolph^1,2, Brian Kuhlman^1,2

¹Department of Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.

Biorxiv : the Preprint Server for Biology

|January 8, 2024

Summary

Protein side chain packing (PSCP) is essential for protein engineering. A new method, PIPPack, uses deep learning for faster and accurate side chain conformation predictions, outperforming existing techniques.

Keywords:

Protein side chain packing deep learning graph neural network message passing

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Area of Science:

Computational biology
Protein engineering
Structural bioinformatics

Background:

Protein side chain packing (PSCP) is vital for understanding protein folding, interactions, and designing novel proteins.
Traditional PSCP methods use rotamer libraries and force fields, while recent deep learning (DL) approaches show improved performance.
Existing DL methods like DLPacker, AttnPacker, and DiffPack have advanced the state-of-the-art in PSCP.

Conclusions:

PIPPack offers a fast and accurate solution for protein side chain packing.
The method's efficiency and performance make it a valuable tool for protein engineering and design.
PIPPack represents a significant advancement in applying deep learning to protein structure prediction.