DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model
Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multi-chain protein complexes. However, modeling a complex structure is challenging particularly when the map resolution is low, typically in the intermediate resolution range of 5 to 10 Å. Within this resolution range, even accurate structure fitting is difficult, let alone de novo modeling. To address this challenge, here we present DiffModeler, a fully automated method for modeling protein complex structures. DiffModeler employs a diffusion model for backbone tracing and integrates AlphaFold2-predicted single-chain structures for structure fitting. Extensive testing on cryo-EM maps at intermediate resolutions demonstrates the exceptional accuracy of DiffModeler in structure modeling, achieving an average TM-Score of 0.92, surpassing existing methodologies significantly. Notably, DiffModeler successfully modeled a protein complex composed of 47 chains and 13,462 residues, achieving a high TM-Score of 0.94. Further benchmarking at low resolutions (10-20 Å) confirms its versatility, demonstrating plausible performances. Moreover, when coupled with CryoREAD, DiffModeler excels in constructing protein-DNA/RNA complex structures for near-atomic resolution maps (0-5 Å), showcasing state-of-the-art performance with average TM-Scores of 0.88 and 0.91 across two datasets..
Medienart: |
Preprint |
---|
Erscheinungsjahr: |
2024 |
---|---|
Erschienen: |
2024 |
Enthalten in: |
bioRxiv.org - (2024) vom: 28. Feb. Zur Gesamtaufnahme - year:2024 |
---|
Sprache: |
Englisch |
---|
Beteiligte Personen: |
Wang, Xiao [VerfasserIn] |
---|
Links: |
Volltext [kostenfrei] |
---|
Themen: |
---|
doi: |
10.1101/2024.01.20.576370 |
---|
funding: |
|
---|---|
Förderinstitution / Projekttitel: |
|
PPN (Katalog-ID): |
XBI042258510 |
---|
LEADER | 01000caa a22002652 4500 | ||
---|---|---|---|
001 | XBI042258510 | ||
003 | DE-627 | ||
005 | 20240229090742.0 | ||
007 | cr uuu---uuuuu | ||
008 | 240124s2024 xx |||||o 00| ||eng c | ||
024 | 7 | |a 10.1101/2024.01.20.576370 |2 doi | |
035 | |a (DE-627)XBI042258510 | ||
035 | |a (biorXiv)10.1101/2024.01.20.576370 | ||
040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
041 | |a eng | ||
100 | 1 | |a Wang, Xiao |e verfasserin |0 (orcid)0000-0003-4435-7098 |4 aut | |
245 | 1 | 0 | |a DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model |
264 | 1 | |c 2024 | |
336 | |a Text |b txt |2 rdacontent | ||
337 | |a Computermedien |b c |2 rdamedia | ||
338 | |a Online-Ressource |b cr |2 rdacarrier | ||
520 | |a Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multi-chain protein complexes. However, modeling a complex structure is challenging particularly when the map resolution is low, typically in the intermediate resolution range of 5 to 10 Å. Within this resolution range, even accurate structure fitting is difficult, let alone de novo modeling. To address this challenge, here we present DiffModeler, a fully automated method for modeling protein complex structures. DiffModeler employs a diffusion model for backbone tracing and integrates AlphaFold2-predicted single-chain structures for structure fitting. Extensive testing on cryo-EM maps at intermediate resolutions demonstrates the exceptional accuracy of DiffModeler in structure modeling, achieving an average TM-Score of 0.92, surpassing existing methodologies significantly. Notably, DiffModeler successfully modeled a protein complex composed of 47 chains and 13,462 residues, achieving a high TM-Score of 0.94. Further benchmarking at low resolutions (10-20 Å) confirms its versatility, demonstrating plausible performances. Moreover, when coupled with CryoREAD, DiffModeler excels in constructing protein-DNA/RNA complex structures for near-atomic resolution maps (0-5 Å), showcasing state-of-the-art performance with average TM-Scores of 0.88 and 0.91 across two datasets. | ||
650 | 4 | |a Biology |7 (dpeaa)DE-84 | |
650 | 4 | |a 570 |7 (dpeaa)DE-84 | |
700 | 1 | |a Zhu, Han |4 aut | |
700 | 1 | |a Terashi, Genki |4 aut | |
700 | 1 | |a Taluja, Manav |4 aut | |
700 | 1 | |a Kihara, Daisuke |4 aut | |
773 | 0 | 8 | |i Enthalten in |t bioRxiv.org |g (2024) vom: 28. Feb. |
773 | 1 | 8 | |g year:2024 |g day:28 |g month:02 |
856 | 4 | 0 | |u http://dx.doi.org/10.1101/2024.01.20.576370 |z kostenfrei |3 Volltext |
912 | |a GBV_XBI | ||
951 | |a AR | ||
952 | |j 2024 |b 28 |c 02 |