The ClusPro web server for protein-protein docking

Abstract

The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.

FIGURE 1

Outline of the ClusPro algorithm. After each step, the number of structures retained is shown in a blue box.

FIGURE 2

Home screen of the ClusPro server. The example shows submission of the job to dock soybean trypsin inhibitor (ligand, PDB ID 1BA7) to the X-ray structure of porcine trypsin (receptor, PDB ID 1QQU).

FIGURE 3

Screen image of the restraint file generator web tool to prepare a JSON file. The generator is available at the URL https://cluspro.org/generate_restraints.html.

FIGURE 4

Screen image of the ClusPro Status page. The screen was obtained by clicking on the job Id on the queue page, for docking of soybean trypsin inhibitor (ligand) to the porcine trypsin (receptor). The Status page shows the job ID number, job name, job status, and submission time stamp. The page also shows pictorial representations of the uploaded and processed input structures The PDB file for the ligand includes two chains, but only chain B is used for docking. Clicking on the labels rec and lig will download the submitted coordinate files as read by the server.

FIGURE 5

Screen image of the ClusPro Results page for docking of soybean trypsin inhibitor (ligand) to the porcine trypsin (receptor). The page shows the job name and, by default, results for the balanced set of scoring function coefficients. Results for electrostatic-favored, hydrophobic-favored, or van der Waals + electrostatics sets can be viewed by clicking the corresponding labels. For each parameter set the result page shows small pictures representing the top 10 models, but the user can display more models (up to 30 or less if fewer than 30 clusters have been created). Clicking on the number above a picture will download that model as a PDB file for your viewing. The page also provides the label to download models for all coefficients.

FIGURE 6

Screen image of the ClusPro Results page showing model scores for the balanced coefficient set when docking soybean trypsin inhibitor to porcine trypsin. The page shows the actual weighting coefficients of the energy terms, and a table that lists the clusters of docked structures in the order of cluster size. For each cluster, the table shows the size (i.e., the number of docked structures), the energy of the cluster center (i.e., the structure that has the highest number of neighbor structures in the cluster), and the energy of the lowest energy structure in the cluster.

FIGURE 7

Visualization by PyMol of the structure at the center of the most populated cluster in docking soybean trypsin inhibitor (ligand) to porcine trypsin (receptor). The docked ligand structure (lig.000.00.pdb) is shown as cyan cartoon, whereas the receptor is shown as grey surface. For comparison we also loaded the X-ray structure of the enzyme-inhibitor complex (PDB ID 1AVX) into PyMol, aligned it with the structure of the receptor, and show the native pose of the inhibitor as magenta cartoon.

FIGURE 8

Screen image of exploring the results of running ClusPro in Others Mode. Results are shown using PyMOL from docking the X-ray structure of the ligand, to the X-ray structure of the FK506 binding protein (FKBP). The receptor, FKBP, is shown as grey surface, and the ligand (lig.003.00.pdb) at center of the largest cluster is shown as cyan cartoon. For comparison we superimposed the native complex (PDB ID 1B6C) on the receptor in the docked structure, and the corresponding ligand pose is shown as magenta cartoon.

FIGURE 9

Screen image of the PyMOL visualization of the results of running ClusPro in Antibody Mode. We docked the X-ray structure of the extracellular domain of the human tissue factor (PDB ID 1TFH) to the unbound X-ray structure of the FAB domain of the inhibitory antibody 5G9 (PDB ID 1FGN). Both the heavy and light chains were used to represent the receptor. The center of the 6^th most populated cluster, lig.000.05.pdb, is shown as cyan cartoon, whereas the antibody is shown in surface representation. The antigen in the native complex (PDB ID 1AHW) is shown as magenta cartoon. The IRMSD between native and predicted ligand poses is 4.7 Å.

FIGURE 10

Best models from docking the signal transducing protein HPr (PDB ID 1POH) to the glucose-specific phosphocarrier protein E2A (PDB ID 1F3G) without and with restraints. The receptor protein, E2A, is shown as grey surface. A. Ligand position at the center of the second largest cluster (shown as cyan cartoon) from docking without restraints. The position is slightly shifted relative to the native ligand binding position, shown as magenta cartoon. B. Ligand position at the center of the largest cluster (shown as blue cartoon) from docking with restraints. The ligand is now turned a few degrees around an axis perpendicular to the center of the receptor.

FIGURE 11

Docking the E. coli PliG lysozyme inhibitor to the salmon goose-type lysozyme using SAXS data as restraints. A near-native model (shown cyan cartoon) was obtained as the center of the 3^rd largest cluster. The X-ray conformation of the inhibitor is shown as magenta cartoon.

FIGURE 12

Constructing the dimer of the sugar aminotransferase AtmS13 from Actinomadura melliaura by homology modeling and multimer docking. Chains A and B of the target dimer are shown in green and light green, respectively. Chain B, predicted from the homology model of chain A with the IRMSD of 2.62 Å, is shown as orange cartoon.

FIGURE 13

Docking of the heparin tetramer probe to the ligand-free structure of the basic fibroblast growth factor. The center of the second largest cluster is shown as cyan sticks. The X-ray structure of the bound hexamer shown in magenta.