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# ![prescott logo](./images/logo-1.png)
# PRESCOTT: Population awaRe Epistatic and StruCtural mOdel of muTational effecTs                                                                                                             

## Introduction
PRESCOTT is a package predicting mutational effects in a protein based on population, evolutionary and structural information.
It is made up of two main programs: escott and prescott.

ESCOTT can calculate effects of single point mutations and multiple point mutations. On the other hand, PRESCOTT incorporates
population frequencies into ESCOTT predictions. Therefore, you need to run ESCOTT first to have predictions of mutational effects. 
We recommend using PRESCOTT via our web site or our docker image. 



## Input Data Requirements

ESCOTT requires two files:
* a multiple sequence alignment (MSA) file in fasta format (mandatory):

    Your query protein must be the first sequence in the fasta file. In addition, the query sequence should not contain any gaps. 

* a structure file in PDB format (optional but recommended)

One of the fastest ways to obtain both input MSA and a PDB file is to run colabfold:
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb

Please note that the MSA file produced by colabfold (a3m file) can contain gaps in the query sequence. You have to remove them before using it in PRESCOTT. You can remove the gaps with pragrams that have a GUI, such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/). 

For testing purpose, you can find example input files for BLAT protein in data/ folder of this repository. 

## Usage
### Running the program
Let's assume that our input MSA is inputAli.fasta and input.pdb is our structure file in PDB format.   

Run the program by issuing the following command in a bash terminal:
```bash
escott inputAli.fasta --pdbfile input.pdb 
```

A quick help can be accessed by typing 
```bash
escott --help
```

By default, ESCOTT will predict the effect of all possible single mutations at all positions in the 
query sequence. Alternatively, a set of single or multiple mutations can be given with the option -m.
Eachline of the file should contain a mutation (e.g. D136R) or combination of mutations separated 
by commas (or colons) and ordered according to their positions in the sequence (e.g. D136R,V271A).

GEMME calls JET2 to compute evolutionary conservation levels. By default, JET2 will retrieve a set
of sequences related to the query, independent from the input set, according to specific criteria.
The retrieval method used in JET2 is PSI-BLAST, which can perform the search either locally (by 
default) or remotely (-r server). Alternatively, the user can provide her/his own psiblast file  
(-r input-b pFile) or her/his own multiple sequence alignment in FASTA format (-r input -f fFile).
JET is run in its iterative mode, iJET, 10 times and the final conservation levels are the maxium 
values obtained over the 10 iterations. 
JET2 configuration file is: default.conf.
JET2 output file is: myProt_jet.res.

## Installation
PRESCOTT is implemented in Python 3 and R. It has been tested only on Linux. Since PRESCOTT has many dependencies, we recommend using our web site or our docker image. If you are a determined user, you can find the steps required to install it from the source in the following link (or in the docs folder of this repository):


# Cite 
Laine E, Karami Y, Carbone A. GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects. Molecular Biology and Evolution, Volume 36, Issue 11, November 2019, Pages 2604–2619
