This paper presents our recent work on developing parallel algorithms and software for solving the global minimization problem for molecular conformation, especially protein folding. Global minimization problems are difficult to solve when the objective functions have many local minimizers, such as the energy functionsfor protein folding. In our approach, to avoid directly minimizing a "difficult" function, a special integral transformation is introduced to transform the function into a class of gradually deformed, but "smoother" or "easier" functions. An optimization procedure is then applied to the new functions successively, to trace their solutions back to the original function. The method can be applied to a large class of nonlinear partially separable functions including energy functions for molecular conformation and protein folding. Mathematical theory for the method, as a special continuation approach to global optimization, is established. Algorithms with different solutions tracing strategies are developed. Different levels of parallelism are exploited for the implementation of the algorithms on massively parallel architectures.