kb/data/en.wikipedia.org/wiki/3D-Jury-0.md

---
title: "3D-Jury"
chunk: 1/1
source: "https://en.wikipedia.org/wiki/3D-Jury"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T14:00:40.841013+00:00"
instance: "kb-cron"
---

3D-Jury is a metaserver that aggregates and compares models from various protein structure prediction servers.
The 3D-Jury algorithm takes in groups of predictions made by a collection of servers and assigns each pair a 3D-Jury score, based on structural similarity. To improve accuracy of the final model, users can select the prediction servers from which to aggregate results. The authors of 3D-Jury designed the system as a meta-predictor because earlier results concluded that the average low-energy protein conformation (by way of aggregation) fit the true conformation better than simply the lowest-energy protein conformation.
The Robetta automatic protein structure prediction server incorporates 3D-Jury into its prediction pipeline.
As of January 2024, the links to 3D-Jury originally hosted by the BioInfoBank Institute are no longer valid.


== Algorithm ==
First, pairwise comparisons are made between every combination of models generated from chosen protein prediction servers. Each comparison is then scored using the MaxSub tool. The score, 
  
    
      
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    {\displaystyle sim(M_{a,b},M_{i,j})}
  
, is generated by counting the number of Cα atoms in the two predictions within 3.5 Å of each other after being superpositioned.
To get a roughly 90% chance two models are of a similar fold class, the authors set a threshold of 40 as the lowest score possible for a pair of models to be annotated as "similar". The authors admittedly chose this threshold based on unpublished work.
There are two scores 3D-Jury gives: the best-model-mode score using one model from each server (
  
    
      
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    {\displaystyle 3D-Jury-single(M_{a,b})}
  
) and the all-model-mode score that considers all models from each server (
  
    
      
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    {\displaystyle 3D-Jury-all(M_{a,b})}
  
).
The best-model-mode score using one model per server, 
  
    
      
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    {\displaystyle 3D-Jury-single(M_{a,b})}
  
, is calculated as,

  
    
      
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    {\displaystyle 3D-Jury-single(M_{a,b})={\frac {\sum _{i}^{N}\max _{j,a\neq i{\mbox{ OR }}b\neq j}^{N_{i}}(sim(M_{a,b},M_{i,j}))}{1+N}}}
  

where 
  
    
      
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    {\displaystyle N}
  
 is the number of servers and 
  
    
      
        
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    {\displaystyle N_{i}}
  
 is the number of top ranking models (with a maximum of 10) from the server 
  
    
      
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    {\displaystyle i}
  
, while a pairwise similarity score is calculated between models 
  
    
      
        
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    {\displaystyle M_{a,b}}
  
 (model 
  
    
      
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    {\displaystyle b}
  
 from server 
  
    
      
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    {\displaystyle a}
  
) and 
  
    
      
        
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    {\displaystyle M_{i,j}}
  
 (model 
  
    
      
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    {\displaystyle j}
  
 from server 
  
    
      
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    {\displaystyle i}
  
).
While the all-model-mode score considering all models from the servers, 
  
    
      
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    {\displaystyle 3D-Jury-all(M_{a,b})}
  
, is calculated as,

  
    
      
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    {\displaystyle 3D-Jury-all(M_{a,b})={\frac {\sum _{i}^{N}\sum _{j,a\neq i{\mbox{ OR }}b\neq j}^{N_{i}}sim(M_{a,b},M_{i,j})}{1+\sum _{i}^{N}N_{i}}}}
  

using similar variables as noted with the best-model-mode score.
Note, these meta-predictor scores do not take into account the confidence scores from each of the models from other servers.


== See also ==
Protein structure prediction
Comparison of software for molecular mechanics modeling
List of protein structure prediction software


== References ==


== External links ==
BioInfoBank Meta Server 3D-Jury web interface