AI model updates | KUAS-SEOUL

EFBALite for 2023

(1) Finding in-silico SELEX model

We had to find some ways to design a specific aptamer for biomarker candidates of cervical cancer, but it was hard to use SELEX, well known precise time-consuming method. To get faster and more efficient ways to design our team’s aptamer, we found EFBALite(software of Vilnius-Lithuania, 2021 iGEM team)

• Lithuania 2021 iGEM wiki

EFBALite is a in-silico SELEX model made by 2021 iGEM team. It generates an aptamer sequence from scratch.

Over a year of iGEM team preparation, the SELEX process can prove to be quite challenging, risky, and time-consuming. It may pose difficulties for future iGEM teams aiming to advance research through SELEX. Therefore, updating EFBALite, an in-silico SELEX model, specifically for Python in the Windows environment in 2023, would be immensely beneficial for upcoming iGEM teams.

(2) Updating EFBALite

When trying to run the model to generate some DNA aptamer sequences for ACTN4 and E7 proteins, there were some problems.

1. Pexpect is a pure Python module for spawning child applications; controlling them, and responding to expected patterns in their output. However, this package did not properly fit to Jupyter Notebook environment because it did not work in the Windows environment 2. So we used Wexpect, which is an alternative version for Pexpect in a window environment, but its version was for Python 2.7, quite different from the latest Python version 3.10

(3) Updated version of EFBALite

The sequences generated initially exhibited a high degree of monotony, such as GTACTACCCCCCCCC and GTTTTTTTTT. As a result, we opted for a more pragmatic approach by seeking SELEXed DNA aptamers based on previous research papers for ACTN4 and E7 proteins. While this endeavor was not directly integrated into the project, we have made available an updated version of "Wexpect" and "EFBALite

• We updated all codes in Python and the Jupyter Notebook environment. Here is the procedure:

First, download the code file from the Vilnius-Lithuania GitHub repository

GitHub

Second, we changed the original EFBALite.py file with our EFBALite.py file. Based on the 2023 version, we have updated the directions for the advanced version library.

from openmm.app import AmberPrmtopFile, AmberInpcrdFile, Simulation, HBonds, PDBFile from openmm import LangevinMiddleIntegrator from openmm.unit import nanometer, kelvin, picosecond, picoseconds, kilojoule_per_mole, angstrom import numpy as np import time from argparse import ArgumentParser, BooleanOptionalAction from functions import generate_target, generate_sequence, compute_spatial_sampling_positions, get_dna_from_topology, move_dna, rotate_dna, compute_initial_entropy, compute_entropy

file[kuas-seoul/updatefiles/EFBALite]

Third, install wexpect. Wexpect is a window version package of Pexpect

pip install wexpect

After installing this package, you need to update some codes because it was built in Python 2. xx version and was not updated. We just changed its outdated functions and library directions.

file[kuas-seoul/updatefiles/weexpect.py]

Last, change generateAmberFiles.py after you install all requirements in https://github.com/igemsoftware2021/Vilnius-Lithuania_Software/tree/main/EFBALite

We changed some Pexpect functions for the Wexpect function, which can be used in Windows environments.

def generate_sequence(dir, target, aptamer, frcmod_file): ''' Generates AMBER files for the specific DNA sequence ''' tleap = wexpect.spawn('tleap') tleap.expect(r'(Welcome to LEaP)') ########################################################### def generate_target(dir, target, frcmod_file): ''' Generates AMBER files for the target ''' tleap = wexpect.spawn('tleap') tleap.expect(r'(Welcome to LEaP)')

file[kuas-seoul/updatefiles/generateAmberFiles.py]