Architectural-constraints-main-data

This repository contains all input/output data needed to reproduce the main results as well as the intermediate analyses in the scientific manuscript Adaptive and Spandrel-like Constraints at Functional Sites in Protein Folds (https://doi.org/10.64898/2026.02.09.704872).

Data structure

We provide a folder (compressed) for each protein family. The general hierarchy of each folder is summarised under data-structure-tree/ if needed, allowing for a clear organisation of all the data. Depending on the analyses carried out for each family and the version of the software used, this may vary slightly. In general, the structure of each family folder is as follows: 

1├── ProteinMPNN

├── ProteinMPNN-ESMFold-FrustraEvo│   ├── Family-target (considering 10 sampling temperature values)│   │   ├── Inputs│   │   └── Outputs│   │       ├── SeqDist3│   │       └── SeqDist12│   ├── Mix (considering the minimun sampling temperature value of both, Family-target and Single-target)│   │   ├── Inputs│   │   └── Outputs│   │       ├── SeqDist3│   │       └── SeqDist12│   └── Single-target (considering 10 sampling temperature values)│       ├── Inputs│       └── Outputs│           ├── SeqDist3│           └── SeqDist12

2├── Caliby-v1 

├── Caliby-ESMFold-FrustraEvo│   └── Family-target (considering the default sampling temperature)│       ├── Inputs│       └── Outputs│           ├── SeqDist3│           └── SeqDist12

3├── Target-structures (the original target structures used as templates for generating reverse-folded protein sequences)

NOTE: Related code and documentation available at https://github.com/miriampol2c/architectural-constraints