Cook, who like Australian skipper Michael Clarke will play his 100th Test in Perth from Friday, said his side retained the belief that they can prevent Australia winning at the WACA to take an unbeatable 3-0 lead in the five-Test series.
"Our confidence has obviously had a hit from the first two Test matches," he told reporters, referring to Brisbane and Adelaide.
"But as a squad we've made a conscious effort to look forward rather than back. We think we've got our preparations right."
Perth is more of a fast-bowlers track and Panesar is expected to miss out, although a team has yet to be announced.
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"We have taken some serious hits but we do have a squad full of people who are determined to turn the ship around, and that's what we must do," Flower said ahead of the game.
Cook refused to speculate on who might be in the starting 11.
"We have a lot of options in the squad, there's a good balance. Whatever team we go in with will be the best one to win the game.