• February 3rd, 2025: FoldScript updated to version 1.1 with many new features (see Version History)
• January 1st, 2025: over 3600 jobs processed in the first three months of the server. Keep spreading the word about FoldScript!
• October 1st, 2024: we are pleased to announce the release of our new Web server: 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 3D protein structures modelled by AlphaFold 2 or 3 in order to assist the user in choosing the most relevant and accurate model. This analysis can be refined by introducing experimentally known 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 enabling the prediction of 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 tedious. Consequently, 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 include previously known experimental data in 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 AlphaFold 2 or 3. 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 enables a large community, whether specialized in structural biology or not, to easily analyze datasets of AI-generated 3D models, and provides rational support in finding the "true best model(s)".
FoldScript is provided as a non-profit service to the scientific community, including commercial users, and may be used 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.
The 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. The authors are not responsible for the use of the results, data or information obtained from this server. This Web server is hosted on the CNRS network and governed by French law. By accessing this website or using all or part of its functions, users formally accept the application of French law. This website does not use tracking cookies or cookies that collect personal data for marketing or analytical purposes (see our 'Cookie Policy'). This website uses an encrypted connection (HTTPS). The IP address of the client computer and the date and time of the connection are processed for usage statistics only. No other data is collected and no data is transferred to third party partners or sites.