Sequence-free domain discovery from cryo-EM density.

Paper · CryoNet.Discovery identifies protein structures from cryo-EM density maps across resolutions through cross-modal recognition.

Input a density map

Upload a low-resolution density region, search structural space without a sequence, and inspect a ranked shortlist with local fitting results.

Launch Discovery Job See the workflow

CryoNet.Discovery workflow Server ready

Density input

Start with one segmented cryo-EM region.

MRC example.mapDensity map · 424 KB Ready

CATHSCOPePDB50AFDBMGnify

Structural retrieval

Search from curated domains to learned structure space.

DateDB retrieval72%

CATH domainsPDB clustersAFDB chains

Candidate assessment

Review ranked candidates and local fitting status.

011e2y_G_0CATH 3.40.30.10Z 4.15
ready

025esy_B_2Local structure fitZ 2.50
ready

036agv_A_0Local structure fitZ 2.11
ready

Density region DateDB search Identified protein

Density-native search

Start from a cryo-EM map instead of a sequence. The server infers density embeddings and retrieves candidate structures from multiple database regimes.

Full ranked candidate list

The result viewer keeps the full top-100 ranked candidate list. Local structures can be viewed and downloaded; candidates without local PDB files remain linked to their source database page.

Built for real screening

One interface covers small curated databases and large-scale AFDB/ESM spaces, so the same page supports validation and exploratory discovery.

Submit A Discovery Job

Upload one cryo-EM density map, choose a target search space, and receive ranked domain candidates together with local fitting outputs where source structures are available.

Tutorial

中文教程 ↗ English Guide ↗

Cryo-EM density map *

Choose file select *.mrc file (<= 2GB)

Database *

Target Name

Email

Ready to Submit

How To Use It

Upload one map Provide one cryo-EM density map in `.mrc`, `.map`, or `.ccp4`-compatible workflow format.

Choose the search space Use domain databases (CATH/SCOPe) or larger PDB50/AFDB/ESM spaces depending on how broad you want the retrieval to be.

Inspect ranked outputs The viewer lists all top-100 candidates. Local hits include fitted downloads, while external-only hits link out to PDB, AFDB, or ESM pages.

Reference

CryoDomain: Sequence-free Protein Domain Identification from Low-resolution Cryo-EM Density Maps , Muzhi Dai, Zhuoer Dong, Weining Fu, Kui Xu#, and Qiangfeng Cliff Zhang#, (2025), the 39rd AAAI Conference on Artificial Intelligence (AAAI), 39, 1.

Dai, M., Xu, K., Fei, Y., Zhang, Y., Yang, R., Lei, J., & Zhang, Q. C. (2026). CryoNet.Discovery identifies protein structures from cryo-EM density maps across resolutions through cross-modal recognition . LangTaoSha Preprint Server.