●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●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

cpxDeepMSA is a deep cascade algorithm to generate high-quality protein complex multiple sequence alignment with high quality, significant depth, a wide range of sequence sources, and strong generalization ability. cpxDeepMSA offered to solve the shortcomings of low-quality cpxMSA results due to the single database and low search depth by using different protein monomer databases and incorporating the three strategies ( genomic distance, phylogeny information, and STRING interaction network) used to join the monomer MSA results of protein complexes.

The output of the cpxDeepMSA server include (An example of the cpxDeepMSA output):

cpxDeepMSA On-line

Input your first sequence below ([30,1000] residues in FASTA format). Example input:


Or upload the sequence from your local computer:

Input your second sequence below ([30,1000] residues in FASTA format). Example input:


Or upload the sequence from your local computer:

Email: (mandatory, where results will be sent to)

ID: (optional, your given name of the protein)

• Download the cpxDeepMSA standalone package
• Download benchmark dataset

• Zi Liu, Dong-Jun Yu. cpxDeepMSA: a deep cascade algorithm for constructing multiple sequence alignment of protein-protein Interactions. submitted, 2022.