EnzyMM Outputļƒ

By default EnzyMM produces a TSV table as output. Optionally PDB structures with matched residues can be written too.

Tip

If you would rather have more compressed and easier to parse output, EnzyMM can alternatively write parquet tables if used with the --write-parquet flag! This relies on the polars library!

Caution

Keep in mind that M-CSA annotations are only available for templates distributed together with EnzyMM. If you design and search with your own templates some annotation fields may be empty.

šŸ–¹ TSV Full Results Tableļƒ

Each row shows data for a match between one of our catalytic templates and the query structure. The table contains the following columns:

  • query_id: str The id of the query - either user provided or derived from the header section of the structure.

  • pairwise_distance: float The pairwise distance threshold at which this match was found in ƅngstrom.

  • match_index: int A running index for each match to a given query.

  • template_pdb_id: str The PDB identifier to the experimental structure from which the template was derived.

  • template_pdb_chain: str The PDB chain or chains from which the template was derived. Refers to the automatically assigned chain identifier in the biological assembly.

  • template_cluster_id: int The id of the conformational cluster to which the template structure belongs.

  • template_cluster_member: int The member index within the cluster. A member might be a partial catalytic site.

  • template_cluster_size: int The total number of members within the cluster.

  • template_effective_size: int The number of specific residues defining the template. Usually equal to the number of side chain interacting residues with specific match codes.

  • template_dimension: int The toal number of residues, including unspecific ones, in the template.

  • template_mcsa_id: int The entry number in the M-CSA to which the template refers. The M-CSA entry can help provide more information about the enzymatic mechanism in question and to trace annotations of the template back to sources in scientific literature.

  • template_uniprot_id: str The UniProt identifier to the protein from which the template was derived. Each template comes from a single protein but some represent homo-multimers.

  • template_ec: list of str Enzyme Commission numbers associated with the template which categorize the enzyme function(s) of the template.

  • template_cath: list of str CATH identifiers to the Protein Structure Classification database describing domains of the template structure.

  • template_multimeric: bool Wether the template contains multiple chains.

  • query_multimeric: bool Wether residues from multiple chains in the query were matched.

  • query_atom_count: int The number of atoms in the query model.

  • query_residue_count: int The number of residues in the query model.

  • rmsd: float Atom-wise Root-mean-square distance in ƅngstrom between atoms matched between the template and the query structure. This metric shows how well the template superposes with the query structure. This metric contributes to filtering 3- and 4-residue matches. Results above 2 ƅ are never returned.

  • log_evalue: float Statistical measure based on RMSD and template size which should be used with caution. Anything less than -4 should be a very good hit and -3 is OK. (E is the expected number of hits at random).

  • orientation: float The mean of pairwise orientation angles in radians between corresponding residues between the template and the query structure. While related to superposition between template and query it is sensitive to changes to important chemical angles determining electrostatic interactions.

  • preserved_order: bool Whether the relative order of residues in the protein sequence of the template and query is identical.

  • completeness: bool Wether all members of the same cluster also matched the query structure. True if there is only one member.

  • predicted_correct: bool Wether the match was predicted to be correct.

  • matched_residues: str The matched residues in the query. The format is [ā€˜3-letter-codeā€™]_[ā€˜chain-identifierā€™]_[ā€˜residue-numberā€™].

  • number_of_mutated_residues: int The number of mutated residues in the template.

  • number_of_side_chain_residues_(template,reference): tuple (int, int) The number of residues in the template which interact through their side chain and (all) the total number of residues including unspecific residues interacting through their main chain.

  • number_of_metal_ligands_(template,reference): tuple (int, int) The number of residues which contribute to metal binding or coordination in the template and the reference. A template composed of mostly metal binding residues is likely less predictive of catalytic function but might indicate a metal binding site.

  • number_of_ptm_residues_(template, reference): tuple (int, int) The number of posttranslationally modified residues in the template and the reference.

  • total_reference_residues: int The number of catalytic residues annotated in the structure the template was derived from. Since a template might only represent a partial catalytic site, this shows how many residues the total site might be composed of.

šŸ–¹ TSV Simple Results Tableļƒ

This table contains a selection of columns of the Full Results Table. Again, each row shows data for a match between one of our catalytic templates and the query structure. The table contains the following columns:

  • query_id: str The id of the query - either user provided or derived from the header section of the structure.

  • pairwise_distance: float The pairwise distance threshold at which this match was found in ƅngstrom.

  • match_index: int A running index for each match to a given query.

  • template_pdb_id: str The PDB identifier to the experimental structure from which the template was derived.

  • template_pdb_chain: str The PDB chain or chains from which the template was derived. Refers to the automatically assigned chain identifier in the biological assembly.

  • template_effective_size: int The number of specific residues defining the template. Usually equal to the number of side chain interacting residues with specific match codes.

  • template_dimension: int The toal number of residues, including unspecific ones, in the template.

  • template_mcsa_id: int The entry number in the M-CSA to which the template refers. The M-CSA entry can help provide more information about the enzymatic mechanism in question and to trace annotations of the template back to sources in scientific literature.

  • template_uniprot_id: str The UniProt identifier to the protein from which the template was derived. Each template comes from a single protein but some represent homo-multimers.

  • template_ec: list of str Enzyme Commission numbers associated with the template which categorize the enzyme function(s) of the template.

  • template_cath: list of str CATH identifiers to the Protein Structure Classification database describing domains of the template structure.

  • rmsd: float Atom-wise Root-mean-square distance in ƅngstrom between atoms matched between the template and the query structure. This metric shows how well the template superposes with the query structure. This metric contributes to filtering 3- and 4-residue matches. Results above 2 ƅ are never returned.

  • orientation: float The mean of pairwise orientation angles in radians between corresponding residues between the template and the query structure. While related to superposition between template and query it is sensitive to changes to important chemical angles determining electrostatic interactions.

  • preserved_order: bool Whether the relative order of residues in the protein sequence of the template and query is identical.

  • predicted_correct: bool Wether the match was predicted to be correct.

  • matched_residues: str The matched residues in the query. The format is [ā€˜3-letter-codeā€™]_[ā€˜chain-identifierā€™]_[ā€˜residue-numberā€™].

  • number_of_metal_ligands_(template,reference): tuple (int, int) The number of residues which contribute to metal binding or coordination in the template and the reference. A template composed of mostly metal binding residues is likely less predictive of catalytic function but might indicate a metal binding site.

  • total_reference_residues: int The number of catalytic residues annotated in the structure the template was derived from. Since a template might only represent a partial catalytic site, this shows how many residues the total site might be composed of.

šŸ–¹ TSV Residue Match Tableļƒ

Each row shows data for one single residue matched between one of our catalytic templates and the query structure. It shows which residues in the query, template and reference corresponded and which catalytic annotatio is associated with this residue. The table contains the following columns:

  • query_id: str The id of the query - either user provided or derived from the header section of the structure.

  • match_index: int A running index for each match to a given query.

  • query_residue: str The residue matched in the query. Format is [ā€˜3-letter-codeā€™]_[ā€˜chain-identifierā€™]_[ā€˜residue-numberā€™].

  • template_pdb_id: str The PDB identifier to the experimental structure from which the template was derived.

  • template_residue: str The corresponding residues in the tempolate. The format is [ā€˜3-letter-codeā€™]_[ā€˜chain-identifierā€™]_[ā€˜residue-numberā€™].

  • reference_pdb_id: str The PDB identifier to the referece experimental structure from which the original annotation was derived.

  • reference_residue: str The corresponding residues in the reference. The format is [ā€˜3-letter-codeā€™]_[ā€˜chain-identifierā€™]_[ā€˜residue-numberā€™].

  • roles: list of str The catalytic roles assigned to this particular residue.

PDB Structuresļƒ

Optionally you can write PDB files for the matches, if you supply the --pdbs flag pointing to a directory. What PDB files will be written depends on if the --transform flag is set.

By default (the --transform flag is not set), one PDB file will be written per query structure with the matches in the coordinate system of the query molecule.

Alternatively if the --transform flag is set, one PDB file will be written per template pdb structure with the matches in the coordinate system of the respective template. This can make superposing multiple matches of different queries with the same template easier.

You can further configure the output in each PDB file with the following two flags: - --include-query: will include the query molecule(s) in the PDB file - --include-template: will include the template(s) in the PDB file

Each match is then added as a subsequent model. By default, matches are written in the query reference frame so that many matches to the same query can we viewed together.

A single match in PDB format will look like this:

REMARK True MATCH 1AMY 0
REMARK TEMPLATE_PDB 1uh3_A
REMARK TEMPLATE CLUSTER 1_1_1
REMARK TEMPLATE RESIDUES 1uh3_A396-A262-A356-A471-A472
REMARK MOLECULE_ID 1AMY
REMARK MATCH INDEX 0
REMARK QUERY COORDINATE FRAME
ATOM   1602  CD  GLU A 204       4.241  63.910  32.378  1.00  7.85           C
ATOM   1603  OE1 GLU A 204       3.145  64.416  32.618  1.00  6.76           O
ATOM   1604  OE2 GLU A 204       5.295  64.536  32.437  1.00 11.92           O
ATOM    673  CG  ASP A  87       0.258  65.949  25.285  1.00  6.24           C
ATOM    675  OD2 ASP A  87       1.453  66.078  25.016  1.00  2.00           O
ATOM    674  OD1 ASP A  87      -0.145  65.786  26.442  1.00  7.47           O
ATOM   1409  CG  ASP A 179       0.050  67.050  30.742  1.00 11.90           C
ATOM   1411  OD2 ASP A 179      -0.640  67.800  31.432  1.00  9.48           O
ATOM   1410  OD1 ASP A 179       1.266  67.144  30.660  1.00 16.59           O

Note

Multiple matches are seperated by MDL and ENDMDL lines!

šŸ”¢ Transformation matricesļƒ

Tip

If you dont want to save aligned PDB structure files for every match, consider instead saving the 4x4 transformation matrix!

By setting the --save-transformations flag, EnzyMM will additionally save a numpy npz file with the transformation matrix using homogenous coorindates. A transformation matrix encodes the rotation and translation needed to align the query structure with the template on the matched residues. To later apply the transformation to your original query structure, you can access this npz file like a dictionary to retrieve a desired matrix by the key <match_index>_

import pyjess
import numpy as np

transformations = np.load("your_transformations.npz")
mol = pyjess.Molecule.load("your_query.pdb")
mol.transform(matrix=transformations[f"{match_index}_{mol.id}_{hit.template.pdb_id}"])

Note

You can also invert the transformation matrix and apply it to the template structure to align the template in the reference frame of the query. Simply invert with numpy.linalg.inv(tfm). This is useful for comparing multiple matches with for the same query.

āš ļø Limitations and Caveatsļƒ

Be critical and apply common sense when interpreting EnzyMM results. Think of template matching as a fast and deterministic approach to identify any structural pattern which satisfies the constraints of the template. Since each template encodes different constraints, interpreting results from many matches is not straightforward. Especially with smaller (and thus less specific) templates, false positives are a real issue. We try to mitigate this issue by applying stringent filtering based on RMSD and residue orientation. Nonetheless, interpret results with caution. Our testing shows a precision in identifying catalytic residues of roughly 80-95% depending on template size.

Given that a template approach is intrinsically limited by the coverage of the template library ā€” or in the case of EnzyMM the coverage of the M-CSA ā€” recall outside of these enzyme families might be limited.

Consider also that EnzyMM makes no prediction of EC number. It simply shows the EC numbers associated with the template. For smaller templates which specify for example metal binding sites or common motifs such as a protein transfer chain or an oxyanion hole, EC prediction might be unreliable. EC numbers particularly at the 4th level become substrate/product specific rather than categorizing enzymatic mechanisms. Often templates are only descriptive up to the 3rd EC level.

Keep in mind that EnzyMM does not include checks for pocket volume or substrate/solvent accessibility. Matches to random non-catalytic arrangements of residues obstructed by other parts of the protein structure are possible. When analyzing predicted protein structures, particular caveats apply. Template matching is particularly sensitive to conformation. Some catalytic arrangements also feature in purely structural metal-binding sites. These can only be distinguished if the coordination sphere of the metal ion is known. Poorly predicted side chain rotamers, unrealistic tertiary structure arrangements and overall protein conformations can severely limit matches EnzyMM can find. Keep in mind that pLDDT does not necessarily reflect on side-chain conformations. Often structures will be relaxed through energy minimization which may impact results.