We developed a multi-touch interface for the citizen science video game Foldit, in which players manipulate 3D protein structures, and compared multi-touch and mouse interfaces in a 41-subject user study. We found that participants performed similarly in both interfaces and did not have an overall preference for either interface. However, results indicate that for tasks involving guided movement to dock protein parts, subjects using the multi-touch interface completed tasks more accurately with fewer moves, and reported higher attention and spatial presence. For tasks involving direct selection and dragging of points, subjects using the mouse interface performed fewer camera adjustments.