Molecular Embedding-Based Algorithm Selection in Protein-Ligand Docking

Quantitative Biology > Quantitative Methods [Submitted on 2 Dec 2025 (v1), last revised 1 Jun 2026 (this version, v2)] Title:Molecular Embedding-Based Algorithm Selection in Protein-Ligand Docking View PDFAbstract:Selecting an effective docking algorithm is highly context-dependent, and no single method performs reliably across structural, chemical, and protocol regimes. MolAS is a lightweight algorithm-selection model that predicts per-algorithm performance from pretrained protein and ligand embeddings using attentional pooling and a shallow residual decoder. With hundreds to a few thousand labelled complexes, MolAS achieves up to a 15 percentage-point absolute improvement over the single-best solver (SBS) and closes 17--66\% of the Virtual Best Solver (VBS)--SBS gap across five docking benchmarks. Analyses of selection frequencies, margin-conditioned reliability, and benchmark-level oracle structure indicate that MolAS is most effective when the workflow-defined oracle landscape has low winner entropy and a reasonably separable top-solver region, but degrades under protocol mismatch that shifts solver rankings and changes the induced labels. These results suggest that, in the evaluated regime, robustness is limited less by representational capacity than by workflow- and protocol-induced instability in solver hierarchies, positioning MolAS as an in-domain selector for fixed pipelines and as a diagnostic tool for assessing when docking algorithm selection is well-posed. Submission history From: Jiabao Brad Wang [view email][v1] Tue, 2 Dec 2025 01:49:17 UTC (1,108 KB) [v2] Mon, 1 Jun 2026 05:23:20 UTC (1,220 KB) Current browse context: q-bio.QM References & Citations Loading... Bibliographic and Citation Tools Bibliographic Explorer (What is the Explorer?) Connected Papers (What is Connected Papers?) Litmaps (What is Litmaps?) scite Smart Citations (What are Smart Citations?) Code, Data and Media Associated with this Article alphaXiv (What is alphaXiv?) CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub (What is DagsHub?) Gotit.pub (What is GotitPub?) Hugging Face (What is Huggingface?) ScienceCast (What is ScienceCast?) Demos Recommenders and Search Tools Influence Flower (What are Influence Flowers?) CORE Recommender (What is CORE?) arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.