In peptide mode, you will need to provide a receptor, a peptide motif and its corresponding peptide sequence. The input receptor should be prepared as described below (See Preparation of Receptor Structures). The selection of the motif is a critical step of our protocol (See Buildup of Motif). Once the motif has been designed and the set of fragments has been extracted, the amino acid sequence is changed back to the actual peptide sequence (using a backbone-dependent rotamer library).
Preparation of Receptor Structures:
Wobbly tails should be removed from the input receptor. The structure of the free receptor is represented as an independent binding unit that is defined as either a single domain, or repeated, non-decomposable domains. Should a protein consist of repeated domains (of the same class), it should be treated as a single unit. If the protein instead consists of different domains, they should be split. Multi-domain proteins may have numerous peptide regulatory sites per domain. For this reason, only the selected domain should be used for docking. An example of domain splitting is shown below (PDB ID: 1EG3). The structure consists of three different domains. Shown in yellow is the single domain used for docking.
Sample motif selection for the peptide HTLKGRRLVFDN with the reported motif RXL.
The peptide motif can also be determined by using the 'Build Motif' button. To use, enter full peptide sequence, e.g. HTLKGRRLVFDN and the reported motif, e.g. RXL. After clicking the 'Build Motif' button, the peptide and motif fields will be generated.
Instead of inputing a motif to utilize our motif-based fragment search, users can upload their own fragment set of peptide structures. Fragment sets should contain no more than 25 pdb files. We recommend that each peptide structure be between 5 and 8 residues long. All pdb files should have the same number of atoms. Fragment sets can be uploaded as a zip or tar file.
After docking, resulting clusters are ranked according to cluster size. In cases where the receptor structure was extracted from a multi-domain protein, solutions that overlap with domain-domain interfaces should be removed. Shown below are predictions for peptide placement on a single domain of a receptor (yellow). The full multi-domain protein (purple) is aligned to the receptor, and results evaluated for domain interference. The predictions which interfere with the other domains are shown in red, and would be disregarded as potential binding sites for the peptide. Valid predictions are displayed in green.
Our lab has developed this protocol using the PeptiDB dataset and the following sequences, motifs, and exclusion lists. Click on the receptor name to download the pdb file. Docking results may be viewed by clicking the corresponding job id. It should be noted that the linked results will contain predictions that have not been processed for domain interference.
Receptor/Chain | Motif | Sequence | Exclusion List | Results |
---|---|---|---|---|
1EG3/A_1 | RXPPX[YF] | RSPPPY | 1EG4 | View Results |
1D1Z/A | TI[YF]XX[VI] | TIYAQV | 1D4T 1D4W 1I3Z 1M27 | View Results |
1OOT/A | PXMPXR | PAMPAR | 1SSH 1Q2V 2B3H 2B3K 2B3L 2BER 2BPA 2BZD 2G6P 2GZ5 2J2F 2NQ6 2NQ7 2X6U 2X6V 2XPY 2XPZ 2XQ0 2XZ0 2XZ1 3T2B 3T2C 3T2D 3T2E 3T2F 3T2G | View Results |
2H3L/A | LDVXV | LDVPV | 1MFG 1MFL | View Results |
2H14/A | ARTKQ | ARTKQ | 2CNX 2CO0 2G99 2G9A 2H13 2H6K 2H6N 2H6Q 2H9M 2H9N 2H9P 2O9K 2XL3 3PSL 4A7J | View Results |
2F1W/A | R[PA]HXS | RAHSS | 2F1X 2FOJ | View Results |
2HPJ/A | DXL[YF]G | DDLYG | 2HPL | View Results |
1CA4/A | PXQXXDD | PQQATDD | 1CZY 1ZMS | View Results |
1JD4/B | A[VTI][AP][YF][YF] | AIAYF | 1JD5 1JD6 | View Results |
1B9K/A_1 | WXX[FY]E | WVTFE | 1W80 2VJ0 | View Results |
1B9K/A_2 | [FY]XDN[FY] | FEDNF | 1KY7 2VJ0 | View Results |
2J2I/B_2 | RXRHXS | RRRHPS | 2C3I 3CXW 3CY2 3CY3 4GW8 | View Results |
1H1R/B | KXRRL | KGRRL | 2CCH 2CCI 2J90 3BHY 3BQR | View Results |
1RWZ/A | QXX[LVI]XXW[FY] | QATLERWF | 1RXZ 2IZO | View Results |
4APE/A | H[LVI][LVI][LVI][YF] | HLLVY | 1ER8 | View Results |
1JWF/A | DXDLL | DEDLL | 1JPL 1JWG 1LF8 3G2U 3G2V | View Results |
A pymol session containing the best results for each of the benchmark cases can be downloaded here: Download Benchmark Results
If you have any questions, please look to see if it is addressed on the help page. If you have any suggestions, please contact us.