●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 ●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

EM-Refiner is a Monte Carlo based method for protein structure refinement and determination using Cryo-EM density map. The pipeline consists of three consecutive steps of structure-to-density map superposition, rigid-body fragment adjustments, and atomic-level structure refinement. During the refinement simulations, the backbone structures are kept flexible with movements guided by a composite of physics- and knowledge-based force field, integrated with Cryo-EM density map data. The pipeline is fully automated and suitable for the protein targets with low-to-medium resolution Cryo-EM density map data.

Input initial structural model (File must be in PDB format, click to download example input) (required):

or





Input density map data (File must be in MRC format, click to download example input) (Note and required):







Please input the resolution of density map (e.g. 10 Å) (required):




Email: (required, where results will be sent to.)

• EM-Refiner standalone package
• EM-Refiner benchmark dataset collected

• Biao Zhang, Xi Zhang, Robin Pearce, Hongbin Shen, Yang Zhang. A new protocol for atomic-level protein structure modeling and refinement using low-to-medium resolution cryo-EM density maps. Journal of Molecular Biology, 432: 5365-5377 (2020) [PDF] [Support Information]