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I-TASSER I-TASSER-MTD C-I-TASSER CR-I-TASSER QUARK C-QUARK LOMETS MUSTER CEthreader SEGMER DeepFold DeepFoldRNA FoldDesign COFACTOR COACH MetaGO TripletGO IonCom FG-MD ModRefiner REMO DEMO DEMO-EM DMFold SPRING COTH Threpp PEPPI BSpred ANGLOR EDock BSP-SLIM SAXSTER FUpred ThreaDom ThreaDomEx EvoDesign BindProf BindProfX SSIPe GPCR-I-TASSER MAGELLAN ResQ STRUM DAMpred

TM-score TM-align US-align MM-align RNA-align NW-align LS-align EDTSurf MVP MVP-Fit SPICKER HAAD PSSpred 3DRobot MR-REX I-TASSER-MR SVMSEQ NeBcon ResPRE TripletRes DeepPotential WDL-RF ATPbind DockRMSD DeepMSA FASPR EM-Refiner GPU-I-TASSER

BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP Tara-3D TM-fold DECOYS POTENTIAL RW/RWplus EvoEF HPSF THE-DB ADDRESS Alpaca-Antibody CASP7 CASP8 CASP9 CASP10 CASP11 CASP12 CASP13 CASP14



DMFold (also known as DMFold-Multimer) is a deep learning-based approach to protein complex structure and function prediction built on deep multiple sequence alignments (MSAs). The core of the pipeline is the integration of DeepMSA2 with the modified structure module of AlphaFold2. Starting from a set of query sequences, DMFold first creates deep monomeric MSAs using an iterative search procedure through multiple whole-genome (Uniclust30 and UniRef90) and metagenome (Metaclust, BFD, Mgnify, TaraDB, MetaSourceDB and JGIclust) databases, where multimeric MSAs are then constructed by pairing the monomeric MSAs based on species annotations. Next, complex structure models are predicted by feeding the multimetic MSAs into the structural modules of AlphaFold2-Multimer, where funtional annotations, including Gene Ontology, Enzyme Commission and Ligand Binding Sites, are generated by COFACTOR2 and US-align based on the top DMFold structure models. DMFold participated (as "Zheng") in CASP15 and ranked as the No. 1 method for protein-protein complex structure prediction, with accuracy significantly higher than the state-of-the-art AlphaFold2 program (i.e., "NBIS-AF2-multimer" in CASP15). Although DMFold focuses on multi-chain protein complexes, it also accepts single-chain monomer sequences (DMFold-Monomer pipeline). The server is freely accessible to all users, including commercial ones. Please report problems and questions at Zhang Lab Server Forum.


CASP: Call for targets for the 2024 CASP modeling experiment [valid till 2024/7/1]


The outputs of the DMFold server include (see Example outputs for complex and Example outputs for monomer):


[Example outputs for complex] [Example outputs for monomer] [Benchmark Dataset] [Standalone package] [Human Proteome] [Check Previous Jobs] [Help] [Forum]

Online server


DMFold News: References:

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