ColabFold

Author	Message
[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 102429 - Posted: 22 Aug 2021, 12:00:40 UTC Interesting project: merge the best parts of AlphaFold2 and RosetTAFold in one solution! And is open source!! ID: 102429 · Rating: 0 · rate: / Reply Quote

Sid Celery Send message Joined: 11 Feb 08 Posts: 2122 Credit: 41,183,435 RAC: 10,025	Message 102430 - Posted: 22 Aug 2021, 13:06:57 UTC - in response to Message 102429. And a nice presentation on it on youtube ColabFold - Making protein folding accessible to all via Google Colab ID: 102430 · Rating: 0 · rate: / Reply Quote

Technologov Send message Joined: 17 Jul 07 Posts: 16 Credit: 415,066,371 RAC: 96,621	Message 102431 - Posted: 22 Aug 2021, 16:19:09 UTC What if I don't have Google Colab, but I have a bunch of my own servers? (CPU+GPU) Which code should I run? ID: 102431 · Rating: 0 · rate: / Reply Quote

Falconet Send message Joined: 9 Mar 09 Posts: 353 Credit: 1,227,479 RAC: 1,836	Message 102432 - Posted: 22 Aug 2021, 17:05:09 UTC - in response to Message 102431. What if I don't have Google Colab, but I have a bunch of my own servers? (CPU+GPU) Which code should I run? I suppose it would be this: https://github.com/RosettaCommons/RoseTTAFold ID: 102432 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 102433 - Posted: 22 Aug 2021, 18:03:13 UTC - in response to Message 102431. What if I don't have Google Colab, but I have a bunch of my own servers? (CPU+GPU) Which code should I run? My first link is to github source of the project... ID: 102433 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 102437 - Posted: 23 Aug 2021, 6:33:40 UTC - in response to Message 102430. And a nice presentation on it on youtube ColabFold - Making protein folding accessible to all via Google Colab Very interesting!! ID: 102437 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 102532 - Posted: 3 Sep 2021, 15:09:32 UTC You can also run Colabfold locally on your pc: localcolabfold ....have an high-end gpu is better... ID: 102532 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 102874 - Posted: 2 Oct 2021, 17:07:51 UTC Last modified: 2 Oct 2021, 17:11:24 UTC Molecular simulation for everyone on Cloud with AlphaFold2, Amber and Charmm support ID: 102874 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 102875 - Posted: 2 Oct 2021, 17:08:49 UTC - in response to Message 102874. Local ColabFold now supports Cuda on Mac OSx ID: 102875 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 103059 - Posted: 30 Oct 2021, 14:29:27 UTC Colabfold results ColabFold offers accelerated protein structure and complex predictions by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold's 20-30x faster search and optimized model use allows predicting thousands of proteins per day on a server with one GPU ID: 103059 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 103166 - Posted: 11 Nov 2021, 14:56:09 UTC Interesting news: Alphafold2_mmseqs2 supports now to complex predictions using Alphafold-multimer. + Template predictions are temporary not possible in the Alphafold2_mmseqs2 notebook. + Advanced (Advaned_beta) notebooks still offer the old complex predictions logic. + ColabFold can be installed locally using pip! ID: 103166 · Rating: 0 · rate: / Reply Quote

robbinespu Send message Joined: 2 Nov 21 Posts: 1 Credit: 11,533 RAC: 0	Message 103181 - Posted: 12 Nov 2021, 7:20:49 UTC - in response to Message 103166. that sound cool ID: 103181 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 105927 - Posted: 13 Apr 2022, 13:06:42 UTC Last modified: 13 Apr 2022, 13:06:55 UTC Some news from the project: + 11Mar2022 We use in default AlphaFold-multimer-v2 weights for complex modeling. + We also offer the old complex modes "AlphaFold-ptm" or "AlphaFold-multimer-v1" + 04Mar2022 ColabFold now uses a much more powerful server for MSAs and searches through the ColabFoldDB instead of BFD/MGnify. ID: 105927 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 106271 - Posted: 25 May 2022, 7:06:28 UTC - in response to Message 105927. ColabFold is now avaiable in COSMIC2 (web platform for submitting cryo-EM jobs through the cloud to Comet, a cluster at the San Diego Supercomputer Center) ID: 106271 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 106332 - Posted: 30 May 2022, 20:07:20 UTC ColabFold publication on Nature ID: 106332 · Rating: 0 · rate: / Reply Quote

[VENETO] boboviz Send message Joined: 1 Dec 05 Posts: 1994 Credit: 9,570,739 RAC: 7,184	Message 108033 - Posted: 8 Feb 2023, 21:08:02 UTC - in response to Message 106332. New version 1.5 (is integrating AlphaFold v2.3.1) ID: 108033 · Rating: 0 · rate: / Reply Quote