MOTIVATION: Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of large protein complexes. Picking single protein particles from cryo-EM micrographs (images) is a crucial step in reconstructing protein structure...
Protein science : a publication of the Protein Society
Mar 1, 2024
Estimating the accuracy of protein structural models is a critical task in protein bioinformatics. The need for robust methods in the estimation of protein model accuracy (EMA) is prevalent in the field of protein structure prediction, where computat...
Methods from artificial intelligence (AI) trained on large datasets of sequences and structures can now "write" proteins with new shapes and molecular functions de novo, without starting from proteins found in nature. In this Perspective, I will disc...
MOTIVATION: Proteins found in nature represent only a fraction of the vast space of possible proteins. Protein design presents an opportunity to explore and expand this protein landscape. Within protein design, protein sequence design plays a crucial...
Protein engineering, design & selection : PEDS
Jan 29, 2024
Sequence design is a crucial step in the process of designing or engineering proteins. Traditionally, physics-based methods have been used to solve for optimal sequences, with the main disadvantages being that they are computationally intensive for t...
Proteins play an important role in life activities and are the basic units for performing functions. Accurately annotating functions to proteins is crucial for understanding the intricate mechanisms of life and developing effective treatments for com...
Database : the journal of biological databases and curation
Jan 19, 2024
The post-translational modifications occur as crucial molecular regulatory mechanisms utilized to regulate diverse cellular processes. Malonylation of proteins, a reversible post-translational modification of lysine/k residues, is linked to a variety...
Compared with proteins, DNA and RNA are more difficult languages to interpret because four-letter coded DNA/RNA sequences have less information content than 20-letter coded protein sequences. While BERT (Bidirectional Encoder Representations from Tra...
MOTIVATION: Protein-protein interaction sites (PPIS) are crucial for deciphering protein action mechanisms and related medical research, which is the key issue in protein action research. Recent studies have shown that graph neural networks have achi...
The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 300k structures released...
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