General Workflow

Part of the weekly release procedure by the PDB is to publish the sequences of the entries to be released the following Wednesday four days earlier. This pre-release is scheduled every Saturday at 3:00 UTC. CAMEO collects the pre-release and, after some pre-processing of the sequences and filtering steps described below, submits a selected set of targets to the registered servers. Participants have until the following Wednesday at 0:00 UTC to return their predictions. Once the reference structures have been released by the PDB the following Wednesday, the evaluation is performed.

Currently CAMEO contains a single category: complex structures modeling (3D). Protein model quality assessment (QE), the old single-chain protein structure (3D), protein contact prediction (CP) and ligand binding site (LB) have been discontinued.

CAMEO servers can be registered as public servers with its full name and results available to everyone, or as development servers, where the name is disguised ('serverX') and all scoring is performed and visible to other method developers, but not to the public. See our complete list of registered servers.

A CAMEO target is a pre-released PDB entry, which is submitted to registered servers. In CAMEO Structures & Complexes, a target consists of one or more peptide, protein, DNA or RNA sequence(s), and zero or more free ligands belonging to the same pre-released PDB entry. A target can, thus, be a monomer, a homo-oligomer or a hetero-oligomer, and contain ligand(s) or not.

CAMEO considers any pre-released sequence containing 30 or more amino acids to be a protein. Amino acid sequences strictly shorter than 30 residues are named peptides. Free ligands are small, non-polymer molecules that are pre-released as InChi codes and SMILES by the PDB.

CAMEO Structures & Complexes only submits complete targets to participating servers, that is targets that only contain types of sequences that the participant can model (protein, DNA, RNA and peptides). CAMEO will never submit part of heteromeric complex.

CAMEO does not know the stoichiometry of complexes, as this information is not part of the PDB pre-release. Participants are expected to predict the complex stoichiometry as part of the modeling.

For instance, a server supporting heteromeric protein modeling will not receive RNA-protein complexes; similarly a server capable of modeling only single protein chains will not receive a heteromeric protein complex as target. The only exception to this is ligands: servers that cannot model ligands can still receive complexes containing ligands (just without the ligand information).

Pre-processing

After downloading the pre-released sequences from the PDB on Saturday, in order to submit a limited number of high-quality targets for modeling, CAMEO Structures & Complexes performs the following actions before submitting the sequences to the participants:

1. Filtering of the sequences
2. Clustering of similar targets
3. Filtering of targets that are too easy

1. Filtering of the sequences

CAMEO Complete Modeling only submits filtered nucleic and amino-acid sequences to the participants. The filtering step removes targets if any of their sequences:

1. contain unknown residues in the canonical sequence;
2. contain non-canonical or modified residues that don't have a parent amino or nucleic acid in the PDB Chemical Component Dictionary;
3. contain non-cannonical nucleic or amino acids (selenocystein, etc.) after the cleanup;
4. contain sequence caps (such as N-terminal acetylation, C-terminal amidation) or contain residues annotated as non-linking by the PDB Chemical Component Dictionary, or linking with a linking type inconsistent with the rest of the sequence;
5. or otherwise couldn't be fully converted to sequences of canonical amino acids.

2. Clustering of similar targets

In order to avoid "duplicate" submissions of very similar targets, CAMEO Structures & Complexes clusters the remaining targets.

First, CAMEO clusters individual polymer sequences from the targets:

1. All protein sequences of 30 amino acids or more are clustered with CD-HIT at 99% sequence identity.
2. All other sequences (nucleic acids, and peptides shorter than 30 amino acids) are clustered based on exact identity.

Then, complexes are clustered based on the set of individual sequences they contain. Complexes that contain the exact same set of sequences are grouped together (clustered complexes).

Finally, a second level of clustering is added to the clustered complexes taking non-polymer ligands into account. Complexes in the same clustered complex are sub-divided into clustered complexes with ligands, each of them containing the exact same set of ligand.

3. Classification of targets

3a. Classification of individual polymer sequences

Target complexes are first classified by difficulty into easy, medium and hard targets.

First, all protein sequences of 30 amino acids or more are searched separately for templates with BLAST against the full list of protein sequences currently in the PDB. Templates are classified into one of three categories:

1. "Easy", if the template has 85% or more sequence identity to the target, and additionally:
   1. at least 70% of the target sequence is covered by the template
   2. and, for target sequences longer than 250 residues, less than 45 amino acids of the target are not covered by the taret-template alignment.
2. "Medium", if the template is not "easy" but has a BLAST hit with an e-value of 10⁴ or less, with the same coverage requirements as for easy targets (70% coverage and less than 45 amino acids not covered for targets longer than 250 residues.
3. "Hard" otherwise.

Second, all nucleic acid sequences and peptide sequences shorter than 30 amino acids are subjected to a template search against all the sequences currently in the PDB. Templates are identified based on exact sequence identity. If a template has the exact same sequence in the PDB it is classified as "easy".

3b. Classification of complexes

CAMEO Structures & Complexes uses the template information obtained from individual sequences and integrates it into a classification of whole complexes.

A template is considered for the complex only if it covers all the sequences of the target and has an a exhaustive (1:1) mapping between every sequence of the target and of the template. The template complex may contain no additional sequences not part the target (or not included in the mapping).

The complex difficulty is defined as follows:

1. "Easy" if a template can be found that is "easy" for all the individual sequences.
   1. "Ligand" targets are target complexes classified as "easy" which contain a novel ligand, that is a ligand which is not present in any of the template that make the complex "easy". (The ligand may however exist in a "medium" or "hard" template. Or a similar ligand may be observed in an "easy" template.)
2. "Medium" if the complex is not "easy", but a template can be found that is either "easy" or "medium" for all the individual sequences.
3. "Hard" if at least one sequence can only be mapped to a "hard" template, or if no template covers the whole complex.

Evaluation

Once the PDB releases the experimental structures on Wednesday (00:00 UTC), we automatically start the evaluation process. Structural information is downloaded from the PDB and the following additional filtering steps are performed:

1. Only solution NMR, X-ray diffraction and high resolution (≤ 4.0Å) EM structures are included in the evaluation. Targets derived from other experimental methods are excluded.
2. Very large complexes (> 200 polymer chains, or > 100 chains of a single entity) are excluded, as current scoring methods are not able to compute them in reasonable time.
3. Emails from participating servers are collected and analyzed, and predictions are scored if the emails were received on time or during the grace period (until Wednesday at 3:00 CET/CEST).

Scores

All the scores are computed with OpenStructure, as described in Studer et al. (2025), with alignments based on residue numbers. Scores are initially computed on every biounit, and only scores against the biounit yielding the highest LDDT (for polymer scores) and resulting in the most ligand scored, highest sum of LDDT-PLI and lowest sum BiSyRMSD (for ligand scores) are kept.

Most scores include a penalty for missing chains and ligands, penalizing methods that fail to predict stoichiometry. Variants considering only mapped chains alleviate this penalty. Besides LDDT, these mapped scores are provided as "Advanced scores" (see below for more details). Note that there are no penalties for added chains or ligands.

The following scores are available:

• The LDDT score (Local Distance Difference Test) evaluates the quality of the local atomic environment of a model of protein or nucleic acid chains. LDDT is superposition independent and considers all atoms in one or more protein and nucleotide chains. LDDT rewards the fraction of correctly predicted inter-atomic distances in a model at different threshold levels. Chains are mapped automatically between the model and the reference, with alignments based on residue numbers. A filter based on the Engh and Huber bond lengths and angles removes stereochemical violations and steric clashes. We use the default inclusion radius (15 Å) and distance difference thresholds (0.5Å, 1Å, 2Å, 4Å).
• LDDT (mapped chains) is a variation of LDDT that only considers mapped chains and hence doesn't penalize for wrong stoichiometry.
• The iLDDT score (interface LDDT) is a variation of LDDT evaluating the accuracy of interfaces by focussing on inter-chain contacts only. ILDDT uses the default LDDT distance cutoffs (0.5Å, 1Å, 2Å, 4Å) and is therefore very stringent and quickly tends to 0 if interaces are modeled incorrectly.
• The TM-score (Template modeling score) is a backbone-only score dependent on a global superposition to assesses the overall accuracy of a complex. It mitigates the effect of outlier regions by focusing on maximizing the alignment of correctly predicted regions, limiting the influence of erroneous regions by treating them as outliers. The TM-score contains a scaling factor d₀ in order to be independent on the protein length. As a result, for large oligomeric complexes, local accuracy can be fairly low even with a high TM-score. In CAMEO, the TM-score is computed with US-align (Zhang et al., (2022)) via OpenStructure.
• The LDDT-PLI score (LDDT Protein-Ligand Interfaces) is a variation of LDDT evaluating the accuracy of polymer-ligand contacts.
• The number of successes is the number of ligand predictions with a BiSyRMSD < 2Å, a symmetry-corrected RMSD after superposition of the binding site, similar to what is commonly defined in the docking community. The number is accompanied with the total number of ligands.

Advanced Scores

The following scores are considered "advanced". They are available in the full data downloads, but are not displayed on the web:

• The QS-score (Quaternary Structure score), initally described by Bertoni et al. (2017), quantifies the fraction of shared interface contacts (residues on different chains with a Cβ-Cβ distance < 12 Å) between two complexes. A QS-score close to 1 translates to very similar interfaces, matching stoichiometry and a majority of identical interfacial contacts. A QS-score close to 0 indicates a radically diverse quaternary structure, probably different stoichiometries and potentially representing alternative binding conformations. The QS-score is symmetrical and considers reference and model identically. Two flavors of QS-score are reported: QS-global where, if the reference is incomplete, contacts that are present only in the model will penalize the score, even though the involved residues are not covered by experiment; and QS-best, which will not penalize contacts missing in the model, even though the involved residues are covered by the reference structure.
• The Complex RMSD is the root mean square deviation of Cα positions (C3’ for nucleic acids) after Kabsch superposition, with a chain mapping optimizing RMSD. RMSD doesn't penalize for missing residues in the model. Because RMSD relies on a global superposition, it can be very sensitive to flexibility.
• The LDDT-LP (LDDT Ligand Pocket) assess the accuracy of the residues in the ligand-binding pocket, irrespective of the ligand, and with a chain mapping optimizing the ligand RMSD. Unlike the LDDT-BS (LDDT Binding Site) computed by earlier versions of CAMEO, it is only computed when a ligand was predicted in or near the binding pocket.
• The mapped scores are scores computed only on chains mapped by the initial chain mapping of the whole complex. They are meant to mitigate the penalty of missing chains for servers that do not predict the stoichiometry of the complexes.

Format Definition

This section describes the requirements for a CAMEO Structures & Complexes server, both on how to receive submissions, and how to return predictions to CAMEO.

Submission

In order to receive submissions your server should be ready to:

1. Receive the target(s) by HTTP POST or GET request.
2. Return a 200 HTTP status code as soon as it receives the target. If your server encounters an error and returns a 4XX or 5XX status code, CAMEO will interrupt the submission. We can manually restart failed submissions on a best-effort basis.

The exact contents of the request depend on the capabilities of your server, and can be customized to some extent.

Prediction

When your server completes the prediction, it should return the model(s) by email to the address that was submitted in the field you registered in the "Results Email (variable name)" field. The following formats are supported:

• For prediction of polymer targets, legacy PDB or mmCIF format, optionally gzipped.
  • The residues must be numbered after the target sequence (usual 1-based numbering). Insertion codes are not allowed.
• For ligand predictions, SDF format, optionally gzipped, separately from the polymer prediction in PDB format.
  • Multiple distinct ligands and ligand copies must be attached in different files.
  • In SDF files containing multiple ligands (separated by $$$$ per SDF format), each molecule will be treated as separate pose of the ligand.
  • All the ligands and poses submitted in SDF format will be scored against the first model (model 1).
• The The CASP15 ligand prediction format is also supported for both polymer and ligand submissions:
  • Model and pose numbers are read from the MODEL and POSE keywords. The MODEL and POSE should contain a 1-based integer number of the model or pose. Only models and poses 1-5 will be processed.
  • The LIGAND keyword is mandatory to mark the beginning of a ligand block. However the number and identification of the ligand are ignored in CAMEO.
  • Up to 5 models OR 5 poses of each ligand per model are supported.
  • Unlike CASP15, it is not possible to match up MODELs and POSEs to return up to 25 predictions per ligand. Only 5 model/poses in total will be analyzed.
  • Unlike CASP16, it is possible to return 1 MODEL with 5 POSEs. There is no need to duplicate the model: CAMEO will do it automatically, and rename the POSEs to the corresponding MODEL number.
  • Unlike other formats in CAMEO, the model number is read from the MODEL keyword, not the ordering of the attachment.
  • The predictions should be preferably send as a single attachment. Separate attachment are also supported, granted that all the data for one model (including ligands) is included in the same file. Ligands in separate files from the polymer model cannot be processed. For that, use the SDF format described above.
  • Other special keywords (such as PFRMAT, TARGET, AUTHOR, METHOD and PARENT) are ignored.

Here are some recommendations regarding the format of this email:

1. Up to 5 models can be returned in PDB or mmCIF format, optionally gzipped.
2. The model(s) should preferably be returned as MIME attachments.
3. Alternatively, a single, uncompressed PDB file can be returned as only data in the body of the email.
4. In case your server returns multiple models as a single multi-model PDB file, each model should begin with the MODEL record, end with the ENDMDL record. Every PDB file should end with an END record.
5. Up to 5 models will be analyzed and scored, but only the first model will be used in aggregated scores and comparisons.
6. You can return several emails. Only the last email received within the submission window will be considered in the evaluation.
7. Make sure the residues are numbered according to the submitted target sequence. Not all scoring methods can realign models.
8. Chain naming is free, but make sure that every chain has a unique name in the model.
9. Please place any free ligand in a separate chain.
10. We only score residues and atoms whose names follow the PDB Chemical Component Dictionary notation. Residues and atom that don't follow this notation will be considered as not modeled.
11. Emails received on Wednesday at 3am (CET/CEST) or later will be ignored in the evaluation.

Note: if your server is registered for the CASP experiment, it should already fulfill most of these technical requirements and you can use the same technology for CAMEO.