2024年9月27日 · As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.

2022年2月11日 · These experimentally determined PPI-hot spots along with available structures have been collected in a database called PPI-Hotspot DB. We have applied the PPI-Hotspot DB to create a nonredundant benchmark, PPI-Hotspot+PDB …

2020年12月9日 · 在转录调控相关的文献中，我们经常能够看到这样的蛋白质相互作用网络（protein protein interaction network，PPI network）。 具体而言，这些相关的文献中首先通过RNA-seq、表达谱芯片或者蛋白质组分析等，找到了在不同分组样本间一系列的差异表达基因或蛋 …

For your target protein provide either a PDB code or a UniProt code. An example of the results for the uniprot O04197 code can be found on this page. Option A) For a known PDB 4-letter code. Option B) For a UniProt code. You can download the entire PPI-HotSpot DB and the associated PPI-HotSpot+PDB BM from this page.

Query all binary protein interactions in a single PDB entry; Get detailed information on protein interaction interfaces of detected structures; Model 3D structures of binary protein interactions using the identified structures as templates.

There are four common approaches for PPI data expansions: 1) manual curation from the biomedical literature by experts; 2) automated PPI data extraction from biomedical literature with text mining methods; 3) computational inference based on interacting protein domains or co-regulation relationships, often derived from data in model organisms; and.

2022年2月28日 · Single-point mutations of certain residues (so-called hot spots) impair/disrupt protein-protein interactions (PPIs), leading to pathogenesis and drug resistance. Conventionally, a PPI-hot spot is identified when its replacement decreased the binding free energy significantly, generally by ≥2 kcal/mo …

Hierarchical Graph Learning for Protein-Protein Interaction. HIGH-PPI runs on Python 3.7-3.9. To install all dependencies, directly run: Download the following whl files to ./file/: torch-scatter, torch-sparse, torch-cluster, torch-spline-conv. Three datasets (SHS27k, SHS148k and STRING) can be downloaded from the Google Drive:

PPIRef is a complete* and non-redundant dataset of protein-protein interactions (PPIs) mined from the Protein Data Bank (PDB). Inspired by the UniRef dataset of protein sequences, PPIRef aims to provide standard data for machine learning on the structures of …

iPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents.