RosettaDock Server Documentation
Tips:
The RosettaDock Server performs a local
docking search. That is, the algorithm will search a set of
conformations near the given starting conformation for the
optimal fit between the two partners. Some suggestions:
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You must upload a reasonable guess for the starting position. Place the protein partners near contact (but not overlapping) with the relevant patches of the proteins facing each other.
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PyMol can be a useful tool to position proteins relative to each other. Use "editing" mode from the right panel, and try right-clicking to select a chain and "drag" to enable translation and rotation of the molecule (typically requiring left-shift + middle and left buttons). Finally from the main menu, File→Export Molecule can be used to write a PDB file containing the starting structure with both docking partners. The ‘align’ command may also be helpful if you are using a homologous complex as a guide.
Alternately, starting positions can be creating using one of several docking servers which perform global searches. Some leading servers include ClusPro, GRAMM-X, HEX, PatchDock, SymmDock, ZDOCK. Note that coordinate file formats from these servers might need to be brought into compliance for use by our server (e.g., putting a TER record between docking partners, assuring that the occupancy field is present and standard atom and residue names are used, etc.).
- Docking partners can be uploaded as two separate PDB files or a single PDB file. If there are multiple chains which serve as a single docking partner (e.g., the heavy and light chains of an antibody), the TER line should be removed between the two chains so that Rosetta knows to treat these as a single partner. Similarly, when creating a combined single input file with both partners, place a TER line between the two partners.
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RosettaDock’s local perturbation includes ~ ±3 Å in the direction between the two proteins, ~ 8 Å in the directions sliding the proteins relative to each other along their surfaces, ~ 8° of tilt of the proteins, and a complete 360° spin around the axis between the centers of the two proteins. The server will start 1000 independent simulations from this range of random positions.
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Given the local nature of the search, there is no need to include extra domains of the proteins beyond the two interacting domains. Trim unneeded residues out of your PDB file before uploading. The server will not accept PDBs larger than 600 residues total.
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A fundamental assumption exploited by RosettaDock is that protein backbone conformations typically do not change much upon association. This holds for many proteins, but not all. If you believe that the backbone of one of your partners is flexible, you should be cautious with the results. For example, docking of a short, flexible peptide (~10 residues) is not likely to work, since a peptide lacks the tertiary interactions which stabilize full-size domains (75-250 residues). Similarly, docking will not capture the flexibility of a molecule like calmodulin; the correct backbone of the protein must be uploaded to begin. Docking of a single amino acid will not produce a reasonable result and is not allowed by the server.
- The PDB file format description can be found here.
- RosettaDock requires all backbone atoms to be present for any residue which appears in the starting structure (missing side-chains are acceptable since they will be rebuit). The error message "missing backbone
atoms" means there are one or more backbone atoms
missing in the input pdb file(s).
Interpreting Results
- The server returns the 10 best-scoring structures from the run in rank order by energy. Click on the [Model-N] link to download the PDB file (see below).
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The server also returns a plot of the energies of all 1000 structures created. Each point on this plot represents a structure created by the server. The x-axis is a distance measure from your starting position, and the y-axis is the score (energy) of the structure. A hallmark of a successful run is an energetic "funnel" of low-energy structures clustered around a single position.
- For convenience, the full set of 1000 decoys is provided as compressed archive files. These decoys are not sorted or filtered.
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For each predicted structure, a PDB file is given. The pdb file has the following sections:
- Coordinates of the design structure
- A list of scores. Many of these scores are used in ab initio structure prediction and are not particularly
relevant to docking. The scores used during docking with the default protocols are:
Low-resolution scores: docking_env: residue environment score docking_pair: residue-residue pair score docking_contact: score based on the number of residue-residue contacts docking_vdw: score for steric clashes docking_site_constraint: score for meeting distance and site constraints docking_fab: score for meeting antibody CDR constraints High-resolution scores: score: the total score using the all-atom (high-resolution) energy function (lower is better) bk_tot: total score used in the side-chain packing algorithm fa_atr: attractive portion of the lennard-jones potential (rewards close contacts) fa_rep: lennard-jones repulsive (penalizes overlaps) fa_sol: lazaridis-karplus solvation model (penalizes buried polars) gsolt: surface-area based solvation model fa_dun: internal energy of side chain rotamers as derived from dunbrack's statistics fa_intra: intra-residue clashes fa_pair: statistics based pair term, favors salt bridges hb_sc: sidechain-sidechain and sidechain-backbone hydrogen bond energy hb_srbb: backbone-backbone hbonds close in primary sequence hb_lrbb: backbone-backbone hbonds distant in primary sequence
- A table of energies for each residue in the protein: totals are at the
bottom
Eatr: lennard-jones attractive Erep: lennard-jones repulsive Esol: lazaridis-karplus solvation energy Eh2o_sol: solvation using explicit water, in default mode (not used) Eaa_phipsi: prob of an aa given phi and psi (not used) Edun: rotamer internal energies Eintra: internal clashes within residues Ehbnd: total hydrogen bonding per residue Epair: pair probabilities derived from the pdb database Eref: reference energy for each amino acid Egb: generalized born solvation energy (not used) Eh2o, Eh2o_hb: energies from explicit waters (not used) Ecst: constraint energies (not used) Eres: total for that residue (lower is better) example of residue energy table: res aa Eatr Erep Esol Eh2o_sol Eaa Edun Eintra Ehbnd Epair Eref Egb Eh2o Eh2o_hb Ecst Eres 1 ALA -0.6 0.2 0.5 0.0 0.0 -0.0 0.0 0.0 0.0 -0.2 0.0 0.0 0.0 0.0 0.2 2 ASP -0.6 0.2 0.4 0.0 -0.1 0.6 0.0 0.0 0.0 0.7 0.0 0.0 0.0 0.0 -0.3 3 GLN -1.3 0.0 0.8 0.0 0.7 0.7 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 4 LEU -3.3 0.0 0.9 0.0 -0.1 0.6 0.0 0.0 0.0 0.1 0.0 0.0 0.0 0.0 -1.9 5 THR -3.2 0.1 2.3 0.0 -0.4 0.0 0.0 -1.2 0.0 0.3 0.0 0.0 0.0 0.0 -2.7 6 GLU -1.8 0.1 1.0 0.0 -0.2 0.9 0.0 -0.8 0.0 0.8 0.0 0.0 0.0 0.0 -1.7 7 GLU -2.2 0.1 1.2 0.0 -0.2 0.9 0.0 -0.8 -0.1 0.8 0.0 0.0 0.0 0.0 -1.9 8 GLN -5.3 0.1 3.3 0.0 -0.1 1.5 0.0 -0.7 -0.1 1.0 0.0 0.0 0.0 0.0 -2.4 9 ILE -4.1 0.1 1.7 0.0 0.0 0.1 0.0 -1.4 0.0 -0.2 0.0 0.0 0.0 0.0 -3.4 10 ALA -2.9 0.1 1.6 0.0 -0.2 -0.0 0.0 -1.6 0.0 -0.2 0.0 0.0 0.0 0.0 -2.9 ... totals -641.0 58.1 339.3 0.0 -29.9 154.2 0.3 -22.2 -16.8 56.6 0.0 0.0 0.0 0.0 -385.6
- A table of: measured energies - expected energies (expected energies are derived
by calculating the average energies of the different amino acids with a certain
number of neighbors in a large set of proteins in the pdb)
This table is useful for determining how well packed a residue is. The column Elj
compares the actual lennard jones energy of residue to the expected value. Well
packed residues should have Elj scores new zero or negative.
Eatr: lennard-jones attractive Erep: lennard-jones repulsive Esol: Lazaridis-Karplus solvation Eaa_phipsi: P(aa|phi,psi) Edun: rotamer preferences from dunbrack's library Eintra: intra residue clashes Ehbnd: hydrogen bonding Epair: statistics based pair term Elj: lennard-jones total Eres: total per residue SASApack: SASApack is related to the void volume in a protein. Surface areas are computed with a 1.4 angstrom probe and 0.5 angstrom probe and the difference (ASA_0.5 - ASA_1.4) is compared to the expected difference for a particular residue type in a particular environment. A negative value is favorable and indicates that the residue is more tightly packed than is seen in average pdb files. example: energies-average(in pdb) energies, AND rsd SASA packing score res aa nb Eatr Erep Esol Eaa Edun Eintra Ehbnd Epair Elj Eres SASApack res_rms sasaprob 1 ALA 3 -0.3 0.1 0.3 0.0 -0.0 0.0 0.0 0.0 -0.2 0.4 2.38 3.97 0.272 2 ASP 6 0.7 -0.1 -0.6 0.1 -1.3 -0.1 0.1 0.1 0.7 -1.1 -3.68 4.09 0.963 3 GLN 10 1.2 -0.3 -0.8 0.8 -2.0 0.0 0.5 0.1 0.9 -1.0 9.17 3.02 0.041 4 LEU 16 0.1 -0.3 -0.5 0.0 -0.7 0.0 0.7 0.0 -0.2 -1.0 6.89 2.56 0.256 5 THR 10 -1.1 -0.2 0.9 -0.3 -0.7 0.0 -0.7 0.0 -1.3 -2.0 -6.11 3.11 0.945 6 GLU 8 0.0 -0.1 -0.2 -0.1 -2.0 0.0 -0.6 0.1 -0.1 -3.3 -4.41 3.03 0.938 7 GLU 9 -0.1 -0.2 -0.2 -0.1 -2.0 0.0 -0.4 0.0 -0.2 -3.1 -2.17 3.69 0.731 8 GLN 16 -1.6 -0.2 0.7 -0.1 -0.9 0.0 0.3 0.0 -1.8 -2.1 -5.18 2.89 0.858 ... avgtot -28.0 4.9 4.5 -0.4 -149.1 -4.7 -42.5 -0.2 -23.1 -243.6 2.28 0.430 - A table of, total measured energies - expected energies, for residues in different
environments: surface, buried and exposed. When designing novel structures we have found it difficult
to get Elj numbers that are zero or negative for the buried residues; this is not necessarily relevant for docking
example: actual-average(in pdb) energies per residue LJatr LJrep Elj buried -0.1 -0.2 -0.3 middle -0.3 -0.1 -0.3 surfac 0.1 -0.1 0.0 - A table of residue-residue pair energies for residues which interact across the docking interface.
Energies are defined the same as in previous tables.
example: Pair energies across interface res1 aa1 res2 aa2 total Eatr Erep Esol Ehbnd Epair Egb Ecst Eplane Eh2o Eh2o_hb B 19 PHE C 812 ARG -0.56 -1.18 0.17 0.45 0.00 0.00 0.00 0.00 0.00 0.00 0.00 B 28 THR C 808 ARG 0.05 -0.01 0.00 0.05 0.00 0.01 0.00 0.00 0.00 0.00 0.00 B 28 THR C 812 ARG 0.01 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 B 30 LYS C 800 TRP 0.04 -0.03 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 B 30 LYS C 801 ARG 0.04 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.00 0.00 0.00 B 30 LYS C 805 VAL -0.51 -0.58 0.00 0.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 B 30 LYS C 808 ARG -0.04 -0.12 0.00 0.05 0.00 0.04 0.00 0.00 0.00 0.00 0.00 B 30 LYS C 809 TYR -0.08 -0.55 0.77 0.74 -1.04 0.00 0.00 0.00 0.00 0.00 0.00
- A table of starting minus finishing χ angles, and absolute χ angles. These can be helpful to detect residues which change rotameric state upon docking. The fraction of residues with unchanged rotamers is also reported.
- Coordinates of the centroid of each docking partner and vectors defining a relative coordinate system between the docking partners.
- φ, ψ and ω angle for each residue
We welcome scientific and technical comments on our server. Please contact DockingServerSupport AT graylab dot jhu dot edu with any comments, questions or concerns.
Happy docking!
