Package: cloudmol
PymolFoldFold your protein in PyMOL!Inspired byColabFoldbySergey O.Visualization inspired bypymol-color-alphafold.Thanks to ESMFold by Meta and theAPI.InfoThe PymolFold service is running on a A5000 instance (cost $100 a week), and the sequence length is limited to 1000aa.Issues and ErrorsIf you encounter any errors or issues while using this project, please don't hesitate to open an issue here on GitHub. Your feedback helps us improve the project and make it more user-friendly for everyone.PymolFold Server: A Shared ResourcePlease note that the PymolFold server is a shared resource, and I request you to use it responsibly. Do not abuse the server, as it can affect the availability and performance of the service for other users.20Sep2023: Add `fold_batch`, a command line tool.
21Aug2023: As the ESMFold API is not stable, the job will be sent to PymolFold server if the job failed.
11Apr2023: `pf_plugin.py` is the PyMOL plugin and the `pf_pkg.py` is a pymol-free python package.
03Dec2022: Add `dms`, `singlemut`, and `webapps`. `pymolfold` allow sequence length up to 700aa.
26Nov2022: ProteinMPNN is now integrated to design proteins.
15Nov2022: I now provide an unofficial API to support user defined recycle number and allow sequence length up to 500aa!Install pymol-open-sourcecondainstall-cconda-forgepymol-open-sourceUsage1. Load extension into PyMOL. In the PyMOL command promptrunhttps://raw.githubusercontent.com/JinyuanSun/PymolFold/main/pf_plugin.py# for user still using python2, it is also py3 compatible, only esmfold supports.runhttps://raw.githubusercontent.com/JinyuanSun/PymolFold/py27/predict_structure.py# try the command below in China mainland, the mirror will be delayed if modifications were just made, download the file to your computer and install it is always a good idea:runhttps://raw.staticdn.net/JinyuanSun/PymolFold/main/pf_plugin.py2. Fold your proteinwebapp avaiable at here, in case someone struggles with using PyMOL.Also, check META'sweb appThecolor_plddtcommand also returns pymolselectionobject of different confidence levels. The color scheme is now compatible with plddt in range (0, 1) and (0, 100) only if they are consistent in your selection.The Meta API (up to 400 aa)esmfoldGENGEIPLEIRATTGAEVDTRAVTAVEMTEGTLGIFRLPEEDYTALENFRYNRVAGENWKPASTVIYVGGTYARLCAYAPYNSVEFKNSSLKTEAGLTMQTYAAEKDMRFAVSGGDEVWKKTPTANFELKRAYARLVLSVVRDATYPNTCKITKAKIEAFTGNIITANTVDISTGTEGSGTQTPQYIHTVTTGLKDGFAIGLPQQTFSGGVVLTLTVDGMEYSVTIPANKLSTFVRGTKYIVSLAVKGGKLTLMSDKILIDKDWAEVQTGTGGSGDDYDTSFN,testcolor_plddt
orientray1280,960,async=1The PymolFold API (up to 500 aa, number of recycle can be set in range (3,24))pymolfoldGENGEIPLEIRATTGAEVDTRAVTAVEMTEGTLGIFRLPEEDYTALENFRYNRVAGENWKPASTVIYVGGTYARLCAYAPYNSVEFKNSSLKTEAGLTMQTYAAEKDMRFAVSGGDEVWKKTPTANFELKRAYARLVLSVVRDATYPNTCKITKAKIEAFTGNIITANTVDISTGTEGSGTQTPQYIHTVTTGLKDGFAIGLPQQTFSGGVVLTLTVDGMEYSVTIPANKLSTFVRGTKYIVSLAVKGGKLTLMSDKILIDKDWAEVQTGTGGSGDDYDTSFN,4,testcolor_plddt
orientray1280,960,async=13. Design Your ProteinThanks toColabDeisgnbySergey O.cpd for sequence generationWebappUsecpdto design seqeunces will fold into the target structure:# commandsfetch1pga.A
cpd1pga.A# output looks like:# >des_0,score=0.72317,seqid=0.6607# PTYKLIINGKKIKGEISVEAPDAKTAEKIFKNYAKENGVNGKWTYDESTKTFTIEE# >des_1,score=0.73929,seqid=0.6250# PTYTLVVNGKKIKGTRSVEAPNAAVAEKIFKQWAKENGVNGTWTYDASTKTFTVTE# >des_2,score=0.72401,seqid=0.6429# PTYTLKINGKKIKGEISVEAPNAEEAEKIFKQYAKDHGVNGKWTYDASTKTFTVTEUsingesmfoldto examin thedes_0:# commandsesmfoldPTYKLIINGKKIKGEISVEAPDAKTAEKIFKNYAKENGVNGKWTYDESTKTFTIEE,1pga_des0super1pga_des0,1pga.Acolor_plddt1pga_des0singlemutfor scoring a signle mutationWebapp# commandsfetch1pga.Asinglemut1pga.A,A,26,F# output maybe (not deterministic):# ================================# mutation: A_26_F, score: -0.0877# ================================dmsforin silicodeep mutational scanWebapp# commandsfetch1pga.Aselectresi1-10dmssele# this might took ~1 min, be pacient ; )# output:# Results save to '/pat/to/working/dir/dms_results.csv'ReferenceESMFold:@article{lin2023evolutionary,title={Evolutionary-scale prediction of atomic-level protein structure with a language model},author={Lin, Zeming and Akin, Halil and Rao, Roshan and Hie, Brian and Zhu, Zhongkai and Lu, Wenting and Smetanin, Nikita and Verkuil, Robert and Kabeli, Ori and Shmueli, Yaniv and others},journal={Science},volume={379},number={6637},pages={1123--1130},year={2023},publisher={American Association for the Advancement of Science}}ProteinMPNN:@article{dauparas2022robust,title={Robust deep learning--based protein sequence design using ProteinMPNN},author={Dauparas, Justas and Anishchenko, Ivan and Bennett, Nathaniel and Bai, Hua and Ragotte, Robert J and Milles, Lukas F and Wicky, Basile IM and Courbet, Alexis and de Haas, Rob J and Bethel, Neville and others},journal={Science},volume={378},number={6615},pages={49--56},year={2022},publisher={American Association for the Advancement of Science}}PyMOL is a trademark of Schrodinger, LLC.