CrossDockingEinrichtungen

CrossDockingEi... is a computational framework for cross-docking experiments in structure-based drug design and protein-ligand modeling. It provides a modular platform to dock ligands into multiple receptor conformations and compare performance across targets within a single workflow.

Developed by a community of researchers to standardize cross-docking benchmarks, CrossDockingEi... aims to improve reproducibility and enable large-scale evaluation of docking algorithms under cross-target conditions, including scenarios where ligands are evaluated against non-cognate protein structures.

The core components include a receptor conformation library, an interface to docking engines, scoring-function adapters, and a results analytics suite. The typical workflow comprises preprocessing of structures, multi-receptor docking runs, generation of cross-docking pairings, and aggregation of metrics such as pose accuracy, success rate, and enrichment. The system emphasizes interoperability with common data formats and established benchmarking datasets.

As an open-source, modular project, CrossDockingEi... supports parallel execution, scripted workflows, and provenance tracking to enhance reproducibility. Its analytics tools provide visualization and statistical summaries to compare docking tools and parameter settings across targets.

Applications include benchmarking docking software, assessing cross-target recognition, and exploring transferability of scoring functions. Limitations include reliance on the quality of input structures, sensitivity to docking parameters and scoring schemes, and the challenge of modeling receptor flexibility in a fully realistic way.