There are many great tools to scan for malware within your web directory. The other alternative available other than Maldet is AI-Bolit. It is a neat tools built using PHP to find viruses, malicious code and hacker’s scripts..

Requirement : PHP5.3 and above

SSH to your server and go to public_html directory

Download AI-Bolit scanner by using links. If you you don’t have it installed, you can install it by running this command

yum -y install links

You can download AI-Bolit from the terminal

links https://revisium.com/aibo

Press down key and navigate to download and select AI-Bolit (General Version) then Save.

Press CTRL + C to exit links. Once downloaded, extract the zip folder

unzip ai-bolit-en.zip
cd ai-bolit

move the scanner to public_html

mv ./* ../
cd ..

run the scanner

php ai-bolit.php

Once the scanning completed. You can locate scan result file in your public_html. You can view the report from the web browser.

example.com/AI-BOLIT-REPORT-_examples_public_html-244453-30-08-2017_23-07.html

I would prefer to rename the file for easy access. Make sure to remove the files once you have performed clean up.