While the input to gLM (context-free protein embedding; ESM2 representation) is identical across all occurrences, gLM’s output (contextualized protein embeddings) cluster with biome types (Fig. 2B; silhouette score = 0.17, see the other 30 multi-biome MGYP visualizations in Supplementary Fig. ...
We supplied four different types of MSAs to AF2: (1) the MSAs generated by using the default AF2 settings, (2) the top paired MSAs constructed using HHblits, described above, (3) both alignments together and finally, (4) the top paired and single-chain MSAs from HHblits to speed up pre...
Nonetheless, the Menin–MLL1 interaction is essential for the biological functions of MLL1 and onco-MLL1. There are two Menin-binding motifs in MLL1, termed as MBM1 (residues 2–15) and MBM2 (residues 23–40) [44], with the former having > 20 × higher binding affinity. A...
ProtCAD ProtCAD is a suite of tools for the design and engineering of novel protein structures, sequences, and functions. It allows users to build and manipulate complex protein structures, generate and evaluate sequence libraries, and simulate mutational effects. ProtCAD is a suite of tools for...
Proteins are diverse biomolecules with a wide variety of structures and functions, and as such, it is a challenge to study them in a high-throughput fashion. There are three major types of protein microarrays: functional, analytical, and reverse phase. Functional protein microarrays are constructed...
Phenolic compounds are ubiquitous plant secondary metabolites that possess various biological activities and are known to interact with proteins, altering their structure and properties. Therefore, interactions between these compounds and proteins has ga
Within cells, proteins seldom act as single isolated species to perform their functions. It has been observed that proteins involved in the same cellular processes often interact with each other [1]. Protein-protein interactions are thus fundamental to almost all biological processes [2]. As advanc...
types of graph curvature: Ollivier Ricci curvature (ORC) and Forman Ricci curvature (FRC). ORC is based on optimal transport theory and captures the geometric properties of a graph [23,38,39,40,41,42,43], while FRC is based on the graph Laplacian and captures the algebraic topological ...
despite the fact that proteins are inherently dynamic and generally adopt multiple conformations to perform their functions9,10. The ability of proteins to interconvert between different conformations is central to their biological activities in all domains of life. The therapeutic effect of drug molecul...
POGLUT1, this systematic review focuses on structural domains and dual function of POGLUT1 along with all possible pathways experimentally observed in specific cell types. It also covers a wide range of literature along with suggestions to highlight the causative role of POGLUTs in human diseases...