DeepMainMast Tutorial: Protein Structure Modeling on Web Server and Google Colab

DeepMainMast
 Tutorial
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Google Colab is a free cloud service from Google that provides an
environment similar to Jupyter Notebooks.
https://github.com/kiharalab/DeepMainMast
https://em.kiharalab.org/algorithm/DeepMainMast
1
DeepMainmast on
EM Server, Google Colab,
 
or
 
Source
 
Code
2
Terashi, Genki, et al. "Integrated Protocol of Protein Structure Modeling for Cryo-EM with Deep Learning and
Structure Prediction." 
bioRxiv
 (2023)
(optional)
 
Registration
 
in Web server
https://em.kiharalab.org
https://em.kiharalab.org/users/registerpage
 You will need to verify your email address to activate the
account. The email will usually arrive instantly, but it might also
take up to 1-2 hours.
Job History
DeepMainmast in Web Server
https://em.kiharalab.org
FAST 24GB GPU card
8-core CPU
No CPU time limitation
Full-atom building & refinement
https://em.kiharalab.org/algorithm/DeepMainMast
Example:
https://em.kiharalab.org/job/viewjob/09f2a6b6a14ad5f210c33abb1c70511c
https://em.kiharalab.org/job/viewjob/1605134d4bdc9c1fcc51e7df4bdda310
4
DeepMainmast in Web Server
5
AF2 models
(optional)
Full-Atom model building & Refinement by
Rosetta (optional)
Contour Level (reduce CPU time)
>2513A
SERIVISPTSRQEGHAELVMEVDDEGIVTKGRYFSITPVRGLEKMVTGKAPETA
PVMVQRICGVCPIPHTLASVEA
>2513B
KPRIGYIHLSGCTGDAMSLTENYDILAELLTNMVDIVYGQTLVDLWEMPEMDLA
LVEGSVCLQDEHSLHELKELREKAKLVCAG
>2513C
VLGTYKEIVSARSTDREIQKLAQDGGIVTGLLAYALDEGIIEGAVVAGPGEEFWK
PQPMVAMSSDELKAAAGTKYTEKLGTVAIPCQTMGIRKMQTYPFGVRFLADKIK
LLVGIYCMENFPYTSLQTFI
Sequence File (FASTA format)
EM map
Chain ID assignment for Homo-oligomer
EMD-1461 (res. 3.8Å)
https://em.kiharalab.org/job/viewjob/a6d42fccb442da686
1365e6d1dd81926
6
Model1: C-alpha Model
Model2: C-alpha Model only confident regions
EMD-1461 (res. 3.8Å)
https://em.kiharalab.org/job/viewjob/a6d42fccb442da686
1365e6d1dd81926
7
Model3: Full-Atom Model
Model4: Full-Atom Model only confident regions
Low confidence region
High confidence region
DeepMainmast Google Colab version
https://github.com/kiharalab/DeepMainMast
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Can not use full-atom model building and refinement.
Limited number of parameter combinations
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Click [Connect GPU]
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Set Job name and input a map file
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Upload a sequence file
11
>2513A
SERIVISPTSRQEGHAELVMEVDDEGIVTKGRYFSITPVRGLEKMVTGKAP
ETAPVMVQRICGVCPIPHTLASVEAIDDSLDIEVPKAGRLLRELTLAAHHVN
SHAIHHFLIAPDFVPENLMADAINSVS
>2513B
KPRIGYIHLSGCTGDAMSLTENYDILAELLTNMVDIVYGQTLVDLWEMPEMD
LALVEGSVCLQDEHSLHELKELREKAKLVCAFGSCAATGCFTRYSRGG
>2513C
VLGTYKEIVSARSTDREIQKLAQDGGIVTGLLAYALDEGIIEGAVVAGPGEEF
WKPQPMVAMSSDELKAAAGTKYTFSPNVMMLKKAVRQYGIEKLGTVAIPC
QTMGIRKMQTYPFGVRFLADKIKLLVGIYCMENFPYTSLQTFI
Optional: Upload AF2 models
12
C
 Model in 3D viewer
13
Low confidence region
High confidence region
DeepMainmast: Command Line
https://github.com/kiharalab/DeepMainMast
Full control of the DeepMainmast pipeline.
Rosetta can generate multiple full-atom models.
Detail Instructions:
https://github.com/kiharalab/DeepMainMast
14
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Explore DeepMainMast for protein structure modeling on web servers like EM Server, Google Colab, or through source code. Gain insights into computational time limits, hardware parameters, model availability, installation process, and integrated protocols. Register on the web server for access and utilize the fast GPU card for efficient full-atom building and refinement. Enhance your modeling experience with Contour Level options and optional features like chain ID assignment and sequence file utilization.


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  1. DeepMainMast Tutorial Protein Structure Modeling: DeepMainmast on Web server https://em.kiharalab.org/algorithm/DeepMainMast DeepMainmast on Google Colab Google Colab is a free cloud service from Google that provides an environment similar to Jupyter Notebooks. https://github.com/kiharalab/DeepMainMast 1

  2. DeepMainmast on EM Server, Google Colab, or Source Code Computatio nal Time Limits Full-Atom Modeling & Refinement Available (Rosetta) Only Ca modeling Confidential ? Installing Hardware Parameters 8 CPU cores GPU (24GB) 2 CPU cores GPU (15GB) 8~ CPU cores GPU (> 10GB) ~4 full-atom Models ~4 Ca Models n/a No unlimited Web Server Automated in notebook ~4 hours (free) Google Colab Yes Python- conda environment Full control ~20 full-atom Models Available (Rosetta) Install code from GitHub Yes unlimited Terashi, Genki, et al. "Integrated Protocol of Protein Structure Modeling for Cryo-EM with Deep Learning and Structure Prediction." bioRxiv (2023) 2

  3. (optional) Registration in Web server https://em.kiharalab.org https://em.kiharalab.org/users/registerpage You will need to verify your email address to activate the account. The email will usually arrive instantly, but it might also take up to 1-2 hours. Job History

  4. DeepMainmast in Web Server https://em.kiharalab.org FAST 24GB GPU card 8-core CPU No CPU time limitation Full-atom building & refinement https://em.kiharalab.org/algorithm/DeepMainMast Example: https://em.kiharalab.org/job/viewjob/09f2a6b6a14ad5f210c33abb1c70511c https://em.kiharalab.org/job/viewjob/1605134d4bdc9c1fcc51e7df4bdda310 4

  5. DeepMainmast in Web Server Contour Level (reduce CPU time) AF2 models (optional) EM map Chain ID assignment for Homo-oligomer Full-Atom model building & Refinement by Rosetta (optional) Sequence File (FASTA format) >2513A SERIVISPTSRQEGHAELVMEVDDEGIVTKGRYFSITPVRGLEKMVTGKAPETA PVMVQRICGVCPIPHTLASVEA >2513B KPRIGYIHLSGCTGDAMSLTENYDILAELLTNMVDIVYGQTLVDLWEMPEMDLA LVEGSVCLQDEHSLHELKELREKAKLVCAG >2513C VLGTYKEIVSARSTDREIQKLAQDGGIVTGLLAYALDEGIIEGAVVAGPGEEFWK PQPMVAMSSDELKAAAGTKYTEKLGTVAIPCQTMGIRKMQTYPFGVRFLADKIK LLVGIYCMENFPYTSLQTFI 5

  6. EMD-1461 (res. 3.8) https://em.kiharalab.org/job/viewjob/a6d42fccb442da686 1365e6d1dd81926 6 Model1: C-alpha Model Model2: C-alpha Model only confident regions

  7. EMD-1461 (res. 3.8) https://em.kiharalab.org/job/viewjob/a6d42fccb442da686 1365e6d1dd81926 Low confidence region High confidence region Model3: Full-Atom Model Model4: Full-Atom Model only confident regions 7

  8. DeepMainmast Google Colab version https://github.com/kiharalab/DeepMainMast Free and confidential. 4-hour limitation. 2CPU cores. 15GB GPU. Can not use full-atom model building and refinement. Limited number of parameter combinations 8

  9. Click [Connect GPU] 9

  10. Set Job name and input a map file 10

  11. Upload a sequence file >2513A SERIVISPTSRQEGHAELVMEVDDEGIVTKGRYFSITPVRGLEKMVTGKAP ETAPVMVQRICGVCPIPHTLASVEAIDDSLDIEVPKAGRLLRELTLAAHHVN SHAIHHFLIAPDFVPENLMADAINSVS >2513B KPRIGYIHLSGCTGDAMSLTENYDILAELLTNMVDIVYGQTLVDLWEMPEMD LALVEGSVCLQDEHSLHELKELREKAKLVCAFGSCAATGCFTRYSRGG >2513C VLGTYKEIVSARSTDREIQKLAQDGGIVTGLLAYALDEGIIEGAVVAGPGEEF WKPQPMVAMSSDELKAAAGTKYTFSPNVMMLKKAVRQYGIEKLGTVAIPC QTMGIRKMQTYPFGVRFLADKIKLLVGIYCMENFPYTSLQTFI 11

  12. Optional: Upload AF2 models 12

  13. Ca Model in 3D viewer Low confidence region High confidence region 13

  14. DeepMainmast: Command Line https://github.com/kiharalab/DeepMainMast Full control of the DeepMainmast pipeline. Rosetta can generate multiple full-atom models. Detail Instructions: https://github.com/kiharalab/DeepMainMast 14

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