Online Services

●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

Accurate identification of structural features of ligand-protein binding is an essential step to characterizing the protein function and developing drugs with optimized sensitivity and specificity. BSP-SLIM is a blind molecular docking method on low-resolution protein structures. The method first identifies putative ligand binding sites by structurally matching the target to the template holo-structures. The ligand-protein docking conformation is then constructed by local shape and chemical feature complementarities between ligand and the negative image of binding pockets.

Click here to download example receptor and ligand structures.
- In this example, the receptor and ligand structures are an I-TASSER model of human deoxycytidine kinase and its ligand, gemcitabine, respectively.
- You can also see the BSP-SLIM output of the example structures here.

NOTE: The server accepts only single protein chain and single ligand for blind docking experiment. - Existence or nonexistence of hydrogens in the receptor structure won't affect the final results. - Existence or nonexistence of hydrogens in the ligand structure won't affect the final results. However, correct assignment of bond orders is recommended. Upload receptor structure file in PDB format from your local computer.    Example of suitable PDB file: example_receptor.pdb Upload ligand structure file in SDF format from your local computer.    Example of suitable SDF file: example_ligand.sdf Email (Mandatory, where results will be sent to)

---

Reference:
Hui Sun Lee and Yang Zhang. BSP-SLIM: A blind low-resolution ligand-protein docking approach using theoretically predicted protein structures, Proteins, 2012, 80:93-110 (download the PDF file).