• October 1st, 2024: we are pleased to announce the release of our new Web server: FoldScript
• October 31st, 2024: more than 1500 jobs processed in the first month. Keep spreading the word about FoldScript!
What is FoldScript?
The FoldScript Web server allows, through a comprehensive and automated analysis, to obtain a synthesis of the primary to quaternary structural information of a set of protein 3D structures modelled by AlphaFold 2 or 3 in order to guide the user in choosing the most relevant and accurate model. This analysis can be refined by introducing experimentally know interaction data.
FoldScript thus offers a large community, specialist or not in structural biology, a rational help in identifying the "real best 3D model(s)" produced by AI predictors.
FoldScript rationale
3D modeling programs using artificial intelligence (AI) have revolutionized structural biology by making it possible to predict protein structures with an unprecedented level of confidence, whether in monomeric or multimeric states and, for some software, in complex with nucleic acids, ligands or ions.
However, these predicted structures remain models and divergences in predictions can be observed between distinct AI modeling algorithms (e.g.AlphaFold 2, AlphaFold 3, RoseTTAFold, ESMFold) as reported in this article.
AlphaFold 2 and 3 generate, by default and for the same run, respectively 25 and 5 different models ranked with a confidence score. Faced with this quantity of data, the task of examining and comparing models is time-consuming and laborious. Worse, in our experience, many users tend to only retain the top-ranked model.
However, it is judicious not to limit ourselves to the model with the best score and, notably, to introduce previously known experimental data into the choice of the most relevant model. Thus, it often appears that the "best" solution proposed by AlphaFold is not always the most reliable and basing our choice solely on confidence scores is far too simplistic.
The FoldScript server was created to respond effectively and rationally to these questions. In this goal, FoldScript performs an automated and detailed analysis of the structural information of the multi-models set produced by an AlphaFold 2 or 3 run. It synthesizes, in a comparative and intelligible flat figure, the primary to quaternary structural information of the models to guide the user in his decision making. In addition, this analysis can be refined by introducing previously known interaction data in order to identify the most relevant model(s).
FoldScript thus allows a large community, specialist or not in structural biology, to easily analyze datasets of 3D models generated by AI and offers rational support in finding the "real best model(s)".
FoldScript is provided as a non-profit service to the scientific community, including commercial users, and can be utilized free of charge for research and educational purposes without restriction.
Send your messages to espript@ibcp.fr, if you have questions, suggestions or issues with this Web server.
Authors make no warranties regarding the correctness of the data. Their responsibility is limited to applying best efforts in providing the most reliable and accurate service. Authors have no responsibility for the use of results, data or information obtained through this server. This Web server is hosted on CNRS network and governed by French law. By visiting this site or using all or part of the site's features, users formally accept the application of French law. This website does not use cookies and uses encrypted HTTP. The client computer IP address as well as connection date and time are processed for usage statistics purpose. No other data are collected and no data are transmitted to third-party partners or sites.
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