Task Force on Mechanisms for Publication and Recording of Methods and Results
Outline (and preliminary draft) statement on publication of high throughput structures
- It is proposed by the Structural Genomics Consortia that deposition of atomic parameters and structure amplitudes be accompanied by a refereed publication. This should be compact and available in electronic form. It should include:
- an account of the protein's expression, purification and crystallisation.
- the essentials describing the crystallographic analysis and the indicators of its quality.
- basic description of the protein's structure and any features of chemical or biological interest, provided by software and/or the authors.
- The preparative and crystallographic information presumably will be available from the tracking procedures.
- The quality of the X-ray analysis and refinement will be assessed by validation software. Such features as the map f.o.m., the connectivity, the Ramachandran angles, the B factor values and their distribution, atom positional errors, uninterpreted electron density, disorder will be generated automatically by the software; authors will be able to annotate this data. These indicators could be formatted into the publication in a standard way.
There will be close liaison with the Validation Task Force headed by Randy Read (we suggest cross-membership).
- The detail in the description should be built on a routine application of software that
- does structure/sequence homology searches
- maps polarity and other properties on to the protein surfaces
- identifies the presence of ligands, cofactors, metal ions
- internal repeats of sequences, motifs and domains
- The authors will be encouraged to add in text any additional features that they identify in their examination of the crystal structure. Particularly useful would be:
- comments on unexplained density
- crystal contacts - relevant to conformation of loops, crystal formation and stability etc
- comments on accuracy in the atomic parameters, disorder and mobility if unusual (these may overlap with the validation exercise).
- when present, interactions between ligands and protein
- comments on protein's function and mechanism of action
- evolutionary and functional links not detected by the software.
The data and associated information should be published electronically, and possibly a hard copy as well if the journals wish. We consider that publication should be undertaken by all interested journals. We are conscious that journals with traditions in handling crystallographic and NMR structures could have useful experience and advantages in the initial stages.
- The report could be modelled on small molecule reports (Acta Cryst. C) or those in Structural and Functional Genomics. Other journals might also be interested.
- The text should be of the order of 500-1000 words, together with legends for figures. More text could be added if necessary, subject to time requirements.
- References will need selection by the authors (is this optional, can this be automated).
- The crystallographic and validation parameters; sequence and structure comparison data etc. will be based on standardised entries (possibly automatic). There should be options to introduce further comments on these computer-automatic outputs.
The report should be examined by members of a panel (to be agreed on) to ensure that the text is accurate, clear and contains genuine insight consistent with the quality of the data and its refinement. Initially the workload will not be too heavy and this will allow a practicable and effective protocol to evolve at a sensible rate.
- The publication should be aimed at maximising the structural and functionally relevant information. We consider that a user-friendly interface with graphic routines would add enormously to the value of the publication. Such routines exist already on the PDB.
- Over the next few years the rate of structure determination will increase. This window will allow us to adapt these proposed mechanisms to a high throughput.