Qifang Xu

Defining the Active Conformation of Typical Protein Kinase Domains from Substrate-Bound PDB Structures Enables Active-State AlphaFold2 Models for All 437 Human Catalytic Protein Kinases

The paper defines structural criteria for the active form of human protein kinases using substrate-bound structures and uses AlphaFold2 to generate active-state models for all 437 human catalytic kinases.

FAM122A ensures cell cycle interphase progression and checkpoint control as a SLiM-dependent substrate-competitive inhibitor to the B55/PP2A phosphatase

This paper identifies FAM122A as a SLiM-dependent inhibitor of B55/PP2A that competes with substrates to regulate cell cycle progression and checkpoint control.

The Protein Common Assembly Database (ProtCAD): A comprehensive structural resource of protein complexes

The paper introduces ProtCAD, a database that clusters protein assembly structures from independent experiments to improve accuracy in biological assembly annotations.

Protein domain-based structural interfaces help interpret biologically-relevant interactions in the human interaction network.

The paper builds a structure-supported human interactome by integrating structural information with PPI data, identifying domain-domain and peptide-binding interactions to improve the resolution and biological relevance of the network.

ProtCID: A data resource for structural information on protein interactions

ProtCID is a database that provides structural information on protein interactions, including domain-level analysis and annotations for clusters of protein interfaces.

Principles and characteristics of biological assemblies in experimentally determined protein structures

The paper analyzes biological assemblies in protein structures, highlighting challenges in determining correct assemblies and recent computational methods that use interface similarity.