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 03:00 (CET/CEST) to return their predictions. Once the reference structures have been released by the PDB the following Wednesday, the evaluation is performed.

The categories supported by CAMEO are the protein structure modeling (3D), protein model quality assessment (QE), and structures and complexes (Beta 3D). Protein contact prediction (CP) and ligand binding site (LB) have been discontinued.0

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 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.

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:

• contain unknown residues in the canonical sequence;
• contain non-canonical or modified residues that don't have a parent amino or nucleic acid in the PDB Chemical Component Dictionary;
• contain non-cannonical nucleic or amino acids (selenocystein, etc.) after the cleanup;
• 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;
• 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:

• "Easy", if the template has 85% or more sequence identity to the target, and additionally:
  • at least 70% of the target sequence is covered by the template
  • and, for target sequences longer than 250 residues, less than 45 amino acids of the target are not covered by the taret-template alignment.
• "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.
• "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:

• "Easy" if a template can be found that is "easy" for all the individual sequences.
  • "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.)
• "Medium" if the complex is not "easy", but a template can be found that is either "easy" or "medium" for all the individual sequences.
• "Hard" if at least one sequence can only be mapped to a "hard" template, or if no template covers the whole complex.

Scores

We are working hard to implement many of the scores from the 3D category into CAMEO Structures & Complexes. We primarily consider superposition-free scores as CAMEO targets might consist of multiple domains or proteins that may not superpose well. So far the following scores are available:

The lDDT score (Local Distance Difference Test on All Atoms) evaluates the quality of the local atomic environment of a model. lDDT rewards the fraction of correctly predicted inter-atomic distances in a model at different threshold levels. lDDT does not depend on a global superposition of the prediction and target structure.
Specifically, interaction distances (cutoff 15 Å) between atoms in the reference protein structure are compared with distances between corresponding atoms in the predictions. If the difference between the two distances is within a defined threshold, the interaction is considered to be preserved in the prediction. The final lDDT-all score is computed by averaging the fraction of correctly modeled interactions for the following four distance difference thresholds: 0.5, 1, 2, and 4 Å (the same thresholds as GDT_HA). A filter based on the Engh and Huber bond lengths and angles removes stereochemical violations and steric clashes. CAMEO additionally offers a Cα - based lDDT score.[ref.: CASP9 TBM Assessment]

The QS-score considers the assembly interface as a whole and is suitable for comparing homo- or hetero-oligomers with identical or different stoichiometries, alternative relative orientations of chains, and distinct amino acid sequences (i.e. homologous complexes). To unequivocally identify the residues of all protein chains in complexes, QS-score first establishes a mapping between equivalent polypeptide chains of the compared structures by exploiting complex symmetries where possible. The resulting QS-score expresses the fraction of shared interface contacts (residues on different chains with a Cβ-Cβ distance < 12 Å) between two assemblies. 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. Targets which cover only part of a hetero-oligomeric complex are not evaluated.

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:

• Receive the target(s) by HTTP POST or GET request.
• 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. Please use our format validation form to find out the exact request that your server will receive. Please fill in the form and the request contents will be shown in the Request Preview section at the very bottom of the form.

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.

Here are some recommendations regarding the format of this email:

• Up to 5 models can be returned in PDB or mmCIF format, optionally gzipped.
• The model(s) should preferably be returned as MIME attachments.
• Alternatively, a single, uncompressed PDB file can be returned as only data in the body of the email.
• 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.
• Up to 5 models will be analyzed and scored, but only the first model will be used in aggregated scores and comparisons.
• You can return several emails. Only the last email received within the submission window will be considered in the evaluation.
• Make sure the residues are numbered according to the submitted target sequence. Not all scoring methods can realign models.
• Chain naming is free, but make sure that every chain has a unique name in the model.
• Please place any free ligand in a separate chain.
• 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.
• 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.