Cloud Hosting

A group of researchers is taking Nature to task for publishing a paper earlier this month about Google DeepMinds protein folding prediction program without requiring the authors publish the code behind the work.

Roland Dunbrack, of Fox Chase Cancer Center in Philadelphia, peer-reviewed the paper but was not given access to code during the review, the authors of a letter submitted today, May 14, to Nature including Dunbrack write, despite repeated requests.

A Nature podcast said AlphaFold3 unlike AlphaFold2 can accurately predict protein-molecule complexes containing DNA, RNA and more. Although the new version is restricted to non-commercial use, researchers are excited by its greater range of predictive abilities and the prospect of speedier drug discovery.

Not everyone was excited. The authors of the letter, which co-author Stephanie A. Wankowicz of the University of California, San Francisco told Retraction Watch was submitted today to Nature, write they were disappointed with the lack of code, or even executables accompanying the publication of AlphaFold3 in Nature. They continue:

Although AlphaFold3 expands AlphaFold2s capacities to include small molecules, nucleic acids, and chemical modifications, it was released without the means to test and use the software in a high-throughput manner. This does not align with the principles of scientific progress, which rely on the ability of the community to evaluate, use, and build upon existing work. The high-profile publication advertises capabilities that remain locked behind the doors of the parent company.

The authors, who are circulating the letter for additional signatures, write that the models limited availability on a hosted web server, capped at ten predictions per day, restricts the scientific communitys capacity to verify the broad claims of the findings or apply the predictions on a large scale. Specifically, the inability to make predictions on novel organic molecules akin to chemical probes and drugs, one of the central claims of the paper, makes it impossible to test or use this method.

A May 8 news story by the independent team of journalists at Nature noted the restrictions. Nature editor in chief Magdalena Skipper told Retraction Watch:

Nature has a long-standing policy designed to facilitate the availability of data, materials and code upon reasonable request. While seeking to enhance transparency at every opportunity, Nature accepts that there may be circumstances under which research data or code are not openly available. When making a decision on data and code availability, we reflect on many different factors, including the potential implications for biosecurity and the ethical challenges this presents. In such cases we work with the authors to provide alternatives that will support reproducibility, for example through the provision of pseudocode, which is made available to the reviewers during peer review.

As noted in the code availability statement in the paper: AlphaFold3 is available as a non-commercial usage only server at https://www.alphafoldserver.com, with restrictions on allowed ligands and covalent modifications. Pseudocode describing the algorithms is available in the Supplementary Information.

The pseudocode, however, will require months of effort to turn into workable code that approximates the performance, wasting valuable time and resources, the authors of the letter write. Even if such a reimplementation is attempted, restricted access raises questions about whether the results could be fully validated.

The authors of the letter continue:

When journals fail to enforce their written policies about making code available to reviewers and alongside publications, they demonstrate how these policies are applied inequitably and how editorial decisions do not align with the needs of the scientific community. While there is an ever-changing landscape of how science is performed and communicated, journals should uphold their role in the community by ensuring that science is reproducible upon dissemination, regardless of who the authors are.

Like Retraction Watch? You can make atax-deductible contribution to support our work,subscribe to our freedaily digestorpaid weekly update,follow uson Twitter, like uson Facebook, or add us to yourRSS reader. If you find a retraction thatsnot in The Retraction Watch Database, you canlet us know here. For comments or feedback, email us at [emailprotected].

Continued here:
Nature earns ire over lack of code availability for Google DeepMind protein folding paper - Retraction Watch