DataCon24/README.md

# DataCon 3.0. Design a Peptide Vector for Drug Delivery

![Project logo](https://t3.ftcdn.net/jpg/04/87/14/48/360_F_487144857_lwRd6hyeEktmt70UOAgojHzlwvY6OgQp.jpg)

## Data description

### 1. Mixed CPPs
   
   Contains CPPs with natural or modified amino acids.

      1.1. POSEIDON
   
      Contains heterogeneous experimental data regarding CPP (natural and non-natural amino acids) activity measurements (.csv format), which are:
      - peptide name,
      - target cell line CPP was tested on cell penetration ability,
      - delivered molecule/protein,
      - paper PubMed ID,
      - cellular uptake measurement + measurement units,
      - CPP+cargo concentration,
      - incubation time,
      - incubation temperature,
      - determination method,
      - uptake type,
      - sequence.

### 2. Natural CPPs
   
   Contains only sequences with natural amino acids.

       2.1. CPPBase
      
       Contains sequences of CPPs with experimentally proved activity in .fasta format.

   
       2.2. Experimental and Experimental2
      
       Contain more sequences of CPPs with experimentally proved activity in .txt format.

   
       2.3. Experimental_high_uptake
      
       Contains CPP sequences with high (but not stated) uptake in .txt format.

       2.4. Balanced_dataset
       
       Represents a balanced dataset of CPPs and non-CPPs; often used for model benchmarking.

### 3. Non-CPPs
   
   Contains negative CPP samples in .txt format.

       3.1. Generated
      
       Contains randomly generated sequences treated as negative.

   
       3.2. Experimental
      
       Contains non-CPP sequences shown not to demonstrate activity experimentally.

### 4. Non-Natural CPPs
   
   Contains CPPs consisting of non-natural amino acids.

       4.1. CPPBase_modified
      
       Contains a list of modified CPPs with experimentally proved activity in .fasta format.

      
       4.2. CPPBase_modified_symbols
      
       Contains a list of abbreviations for modified amino acids  in .txt format (ABBREVIATION: NAME; ...: ...).


## Useful tools

### Structure prediction

   In the relevant folder you can find a Jupiter notebook with AlphaFold 2. 
   
   Just insert the sequence

   ![insert sequence](https://github.com/acid-design-lab/DataCon24/assets/82499756/607ad1b2-0b29-4490-8771-76de5fd6f9b3)

   and get a 3D structure!

   ![3d structure](https://github.com/acid-design-lab/DataCon24/assets/82499756/93b60dd2-b627-4c46-82c9-6127af4e26bb)