Opened 4 years ago

Closed 4 years ago

#6312 closed enhancement (fixed)

ColabFold-MMSEQs2 notebook much faster than AlphaFold2 notebook

Reported by: Tristan Croll Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.4.dev202203030220 (2022-03-03 02:20:09 UTC)
Description
General-interest/FYI: I ran a test yesterday, generating predictions for the same antibody (heavy and light chain as a complex) via the official AlphaFold2 notebook and via the ColabFold-MMSEQs2 notebook at https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb. The speed difference is stark - my conservative estimate is that I could have run at least five predictions on the ColabFold notebook in the time it took to run one on the official AlphaFold one. It's almost all in the MSA step - where MMSEQS2 took about 5 minutes, JACKHMMER took about 2 and a half hours. The resulting models were to all intents and purposes identical. 

Log:
> isolde shorthand

isolde is provided by the uninstalled bundle ISOLDE version 1.3  
UCSF ChimeraX version: 1.4.dev202203030220 (2022-03-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 497.29
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Locale: en_GB.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: Notebook                        
Model: P7xxTM1
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 68,654,501,888
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
OSLanguage: en-GB

Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.9.1
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    blockdiag: 3.0.0
    certifi: 2021.10.8
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    ChimeraX-Alignments: 2.2.3
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Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Performance
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ColabFold-MMSEQs2 notebook much faster than AlphaFold2 notebook

comment:2 by Tom Goddard, 4 years ago

Component: Performance → Structure Prediction
Resolution: → fixed
Status: assigned → closed
Type: defect → enhancement

Yeah, I have wanted to try mmseq2 with AlphaFold for about 3 months after I saw the biorxiv paper on it. The sequence alignment step does take about half the time and the standard AlphaFold approach of jackhmmer and hhblits may not be best. I especially want to try mmseq2 for the sequence search and alignments because hhblits fails in some cases preventing any structure prediction with some sequences with standard AlphaFold. There are many other AlphaFold issues so I don't expect I'll be looking at mmseq2 for at least a month, more likely 6 months.

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