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MultiFOLD2, ModFOLDdock2 and MultiFOLD2_refine: prediction, quality assessment and refinement of protein tertiary and quaternary structure models

\n\nA docker container for the MultiFOLD2, ModFOLDdock2 and MultiFOLD2_refine methods developed by the McGuffin group for CASP16.\n\n

Please cite the relevant papers:

\n\nMultiFOLD2 and ModFOLDdock2:\nMcGuffin, L. J., Alhaddad, S. N., Behzadi, B., Edmunds, N. S., Genc, A. G., and Adiyaman, R. (2025) Prediction and quality assessment of protein quaternary structure models using the MultiFOLD2 and ModFOLDdock2 servers. Nucleic Acids Research, gkaf336. DOI PubMed\n \nMultiFOLD:\nMcGuffin, L. J., Edmunds N. S., Genc, A. G., Alharbi, S. M. A., Salehe, B. R. and Adiyaman, R. (2023) Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers. Nucleic Acids Research. gkad297. DOI PubMed\n\nModFOLDdock:\nEdmunds, N. S., Alharbi, S. M. A., Genc, A. G., Adiyaman, R. and McGuffin, L. J. (2023) Estimation of Model Accuracy in CASP15 Using the ModFOLDdock Server. Proteins, Epub ahead of print. DOI PubMed\n\nMultiFOLD_refine:\nAdiyaman, R., Edmunds, N. S., Genc, A. G., Alharbi, S. M. A. and McGuffin, L. J. (2023) Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process. Bioinformatics Advances, vbad078. DOI \n\nNote: For ModFOLDdock2Q, the lightweight version of ModFOLDdock2, click here\n\n

Requirements

\n\nThe latest version of Docker and the NVIDIA Container Toolkit.\n\nNOTE: This version has been tested to work on Ubuntu 22.04 with NVIDIA L40S GPUs.\n\n

Setup

\nOptionally set the input and output paths in your shell (alternatively just include the full paths when you run):\n\nexport MF2_IN=/location/for/your/input/fasta_files/\n\nexport MF2_OUT=/location/for/your/output/files/\n\n(Note: The commands below can be also be run without sudo by following the Docker Engine post-installation steps.)\n\n

Run standard MultiFOLD2 for 3D modelling of multimers from sequences in FASTA format

\n\nsudo docker run --gpus all -v $MF2_IN:/MultiFOLD2_input -v $MF2_OUT:/MultiFOLD2_output mcguffin/multifold2 /MultiFOLD2/run_MultiFOLD2_docker.sh targetname fastafile stoichiometry\n\ne.g. Run MultiFOLD2 for CASP16 target \"H0232\" with the FASTA file \"H0232.fasta\" and stoichiometry \"A2\" as follows:\n\nsudo docker run --gpus all -v $MF2_IN:/MultiFOLD2_input -v $MF2_OUT:/MultiFOLD2_output mcguffin/multifold2 /MultiFOLD2/run_MultiFOLD2_docker.sh H0232 H0232.fasta A2B2\n\nNote: regarding the stochiometry parameter, a monomer=A1, a homodimer=A2, a homotrimer=A3, etc. A heterodimer=A1B1, a heterotrimer=A1B1C1, etc. You can also model targets with more complex stoichiometries, such as a dimer of dimers=A2B2, a trimer and dimer=A3B2, a nonamer and trimer=A9B3, and so on. You must provide a sequence in the FASTA file for each subunit in your complex. If the stoichiometry is not known, then you can use the parameter \"unknown\" and it will be predicted from templates, e.g.,\n\nsudo docker run --gpus all -v $MF2_IN:/MultiFOLD_input -v $MF2_OUT:/MultiFOLD_output mcguffin/multifold /MultiFOLD/run_MultiFOLD_docker.sh H0232 H0232.fasta unknown\n\nMultiFOLD2 output:\nThe output for each job will be found in $MF2_OUT within a unique subdirectory named according to the time and date of submission plus the extension \"\\_TS\". Your final results file will be in CASP TS format and can be found within the \"MultiFOLD2_TS_\" subdirectory with a filename containing the unique sequence ID for your job and ending with the extension \"_TS.txt\" e.g.\n\n$MF2_OUT/14_52_44_883_18-1-2025_TS/MultiFOLD2_TS_r28d3fk5p89l3fvc/r28d3fk5p89l3fvc_TS.txt\n\nAll 3D models in PDB format can be found within the MultiFOLD_models/ subdirectory e.g.\n\n$MF2_OUT/14_52_44_883_18-1-2025_TS/MultiFOLD2_TS_r28d3fk5p89l3fvc/MultiFOLD2_models/\n\nThe final top 5 models and ranking data can be found in the final_TS_data/ subdirectory e.g.\n\n$MF2_OUT/14_52_44_883_18-1-2025_TS/final_TS_data/\n\n

Run MultiFOLD2_refine for refining 3D models of complexes with known stoichiometry

\n\nsudo docker run --gpus all -v $MF2_IN:/MultiFOLD2_input -v $MF2_OUT:/MultiFOLD2_output mcguffin/multifold2 /MultiFOLD2/run_MultiFOLD2_refine_docker.sh targetname fastafile modelfile stoichiometry recycles\n\ne.g. Run MultiFOLD2_refine for CASP15 target \"H1232\" with the FASTA file \"H1232.fasta\" on the model \"H1232TS163_1.pdb\" with stoichiometry \"A2B2\" for \"12\" recycles as follows:\n\nsudo docker run --gpus all -v $MF2_IN:/MultiFOLD2_input -v $MF2_OUT:/MultiFOLD2_output mcguffin/multifold2 /MultiFOLD2/run_MultiFOLD2_refine_docker.sh H1232 H1232.fasta H1232TS163_1.pdb A2B2 12\n\nMultiFOLD2_refine output:\nThe output for each job will be found in $MF2_OUT within a unique subdirectory named according to the time and date of submission plus the extension \"\\_REF\". Your final results file will be in CASP TS format and can be found within the \"MultiFOLD2_TS_\" subdirectory with a filename containing the unique sequence ID for your job and ending with the extension \"_TS.txt\" e.g.\n\n$MF2_OUT/14_52_44_883_18-1-2025_REF/MultiFOLD2_TS_r28d3fk5p89l3fvc/r28d3fk5p89l3fvc_TS.txt\n\nAll 3D models in PDB format can be found within the MultiFOLD2_models/ subdirectory e.g.\n\n$MF2_OUT/14_52_44_883_18-1-2025_REF/MultiFOLD2_TS_r28d3fk5p89l3fvc/MultiFOLD2_models/\n\n

Run ModFOLDdock2 for estimating the quality of 3D models of complexes

\n\nsudo docker run --gpus all -v $MF2_IN:/MultiFOLD2_input -v $MF2_OUT:/MultiFOLD2_output mcguffin/multifold2 /MultiFOLD2/run_ModFOLDdock2_docker.sh targetname fastafile modelfile stoichiometry\n\nFor estimating the quality of a single model:\n\ne.g. Run ModFOLDdock for CASP15 target \"H1232\" with the FASTA file \"H1232.fasta\" on the single model \"H1232TS163_1.pdb\" with stoichiometry \"A2B2\" as follows:\n\nsudo docker run --gpus all -v $MF2_IN:/MultiFOLD2_input -v $MF2_OUT:/MultiFOLD2_output mcguffin/multifold2 /MultiFOLD2/run_ModFOLDdock2_docker.sh H1232 H1232.fasta H1232TS163_1o.pdb A2B2 \n\nFor estimating the quality of multiple models:\n\ne.g. Run ModFOLDdock for CASP15 target \"H1232\" with the FASTA file \"H1232.fasta\" on multiple models \"H1232.tar.gz\" with stoichiometry \"A2B2\" as follows:\n\nsudo docker run --gpus all -v $MF2_IN:/MultiFOLD2_input -v $MF2_OUT:/MultiFOLD2_output mcguffin/multifold2 /MultiFOLD2/run_ModFOLDdock2_docker.sh H1232 H1232.fasta H1232.tar.gz A2B2\n\nModFOLDdock2 output:\nThe output for each job will be found in $MF2_OUT within a unique subdirectory named according to the time and date of submission plus the extension \"\\_QA\". Your final results file will be in CASP15 QA format and can be found within this subdirectory with a filename containing the unique sequence ID for your job and ending with the extensions: \"_QA.txt\" for standard ModFOLDdock2 jobs, \"_R_QA.txt\" for ModFOLDdock2R jobs, or \"_S_QA.txt\" for ModFOLDdock2S jobs e.g.\n\n$MF2_OUT/14_52_44_883_18-1-2025_QA/r28d3fk5p89l3fvc_QA.txt\n\n$MF2_OUT/14_52_44_883_18-1-2025_QA/r28d3fk5p89l3fvc_R_QA.txt,\n\nor\n\n$MF2_OUT/14_52_44_883_18-1-2025_QA/r28d3fk5p89l3fvc_S_QA.txt\n\n

Contact

\nProf. Liam J. McGuffin\n\n

License

\n\nMIT License\n\nCopyright (c) 2025 Liam McGuffin, Recep Adiyaman, and the University of Reading\n\nPermission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: \n\nThe above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. \n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n\nThird-Party Software Notices for MultiFOLD2 Docker image\n","has_starred","hub_user","immutable_tags_settings",{"_78":11,"_79":80},"enabled","rules",[81],".*","is_automated","permissions",{"_85":17,"_86":11,"_87":11},"read","write","admin","user","storage_size",81598817027,"orgData","recentTags",[94],{"_95":48,"_96":97,"_98":99,"_100":101,"_102":103,"_104":105,"_54":121,"_122":97,"_123":29,"_124":60,"_39":125,"_126":127,"_128":112,"_129":121,"_130":69,"_131":17},"content_type","creator",1506247,"digest","sha256:13ddbc668bebfd472d1cf4fc28f6b478ecf3be9f2c7dfece265a5a7e08e4f932","full_size",81598809118,"id",831885213,"images",[106],{"_107":108,"_98":99,"_109":110,"_111":112,"_113":114,"_115":116,"_117":110,"_118":-5,"_119":101,"_66":69,"_120":-5},"architecture","amd64","features","","last_pulled","2026-09-26T14:56:14.220418171Z","last_pushed","2025-01-18T21:36:28.247957553Z","os","linux","os_features","os_version","size","variant","2025-01-18T21:36:28.679184Z","last_updater","last_updater_username","media_type","latest","repository",26223770,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":143,"_152":153,"_139":162,"_163":11},{"_36":144,"_46":147,"_49":50,"_51":52,"_53":11,"_54":55,"_56":57,"_58":148,"_39":31,"_28":29,"_61":62,"_63":48,"_64":65,"_66":67,"_68":69,"_70":-5,"_71":65,"_72":73,"_74":11,"_75":29,"_76":149,"_82":11,"_83":151,"_88":29,"_89":90},[145,146],{"_39":40,"_41":42},{"_39":44,"_41":45},[48],[60],{"_78":11,"_79":150},[81],{"_85":17,"_86":11,"_87":11},"tags",{"_154":67,"_155":-5,"_156":-5,"_157":158},"count","next","previous","results",[159],{"_95":48,"_96":97,"_98":99,"_100":101,"_102":103,"_104":160,"_54":121,"_122":97,"_123":29,"_124":60,"_39":125,"_126":127,"_128":112,"_129":121,"_130":69,"_131":17},[161],{"_107":108,"_98":99,"_109":110,"_111":112,"_113":114,"_115":116,"_117":110,"_118":-5,"_119":101,"_66":69,"_120":-5},[],"canDeleteTags","actionData","errors"]

mcguffin/multifold2

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