CryptoBench: cryptic protein-ligand binding sites dataset and benchmark.

ABSTRACT:

Motivation

Structure-based methods for detecting protein-ligand binding sites play a crucial role in various domains, from fundamental research to biomedical applications. However, current prediction methodologies often rely on holo (ligand-bound) protein conformations for training and evaluation, overlooking the significance of the apo (ligand-free) states. This oversight is particularly problematic in the case of cryptic binding sites (CBSs) where holo-based assessment yields unrealistic performance expectations.

Results

To advance the development in this domain, we introduce CryptoBench, a benchmark dataset tailored for training and evaluating novel CBS prediction methodologies. CryptoBench is constructed upon a large collection of apo-holo protein pairs, grouped by UniPr

SUBMITTER: Skrhak V 

PROVIDER: S-EPMC11725321 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature