Happily, there is a great deal of information out there online about players' gear and tones. It's not always accurate -- there can be a lot of weird speculation especially about the gear and tones on older recordings. My experience, though, is that a lot of modern players (and I'm counting Daron Malakian, even though the
Mezmerize/Hypnotize album(s) was/were, like, from 16 years ago!) are happy to talk about their gear, especially in interviews and features with well-known guitar magazines, YouTube interviewers, etc.
So, for example, there is a
Guitar World feature on/interview with Malakian from that period (
https://www.guitarworld.com/features/daron-malakian-21st-century-schizoid-man) that suggests his main gear on the album was a modded Marshall "JMP100". That designation is a little hazy, but it's probably some kind of '70s Marshall, either a non-master-volume Superlead or an early master-volume 2203. There are a few AmpliTube options here, but I'd pick a
Vintage Metal Lead or -- for a more "modern" and "modded" sound -- the
AFD 100. More recent interviews with Malakian suggest he's into Friedman amps, feeling they sound like his modded Marshalls, and so the
MiniPlex 20 (based on a Friedman Pink Taco) might be a good option, too.
The same
GW article says he used a single 4x12 cab, and there's a more recent Ernie Ball YouTube video (
https://www.youtube.com/watch?v=QfPYrloYyUs) that (among other things) shows Malakian playing with a Marshall cab of the angled "A" variety, though I wouldn't want to guess exactly which cab model or what speakers might be in it. You can just try different Marshall-style cabs in AmpliTube and see what sounds good to you. That video does seem to show him using a single Royer 121 on the cab, though, which is modeled in AmpliTube as the
Ribbon 121. The video also shows his pedalboard: it's not super complicated. There are is a Boss DD-6 (AmpliTube's
/Delay I think models the DD-3), another Strymon digital delay (not modeled in AmpliTube but ... it's another digital delay), and a MXR Phase 90 (model in AmpliTube as the
Phaze Nine).
The
GW article also discusses some esoteric room-mic'ing techniques and notes that some of the more exotic "multitracked, harmonized, Greek bouzouki-like timbres [on the
Mezmerize/Hypnotize album(s)] ... were achieved on a Fender Jazzmaster through a Divided by 13 model FTR-37 amp" -- but it's probably best to not worry about all that too much!
Anyway, I really don't know much about Malakian or SOAD, but a little Googling will quickly start to get you some information about his gear. Start there and experiment.