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Estimating the boost-phase trajectory of a ballistic missile using line of sight measurements from space-borne passive sensors is an important issue in missile defense. A well-known difficulty of this issue is the poor-observability of the target motion. A profile-based maximum penalised likelihood estimator is presented, which is expected to work in poor-observability scenarios. Firstly, a more adaptable boost-phase profile is proposed by introducing unknown parameters. Then, the estimator is given based on the Bayesian paradigm. After that, a special penalty for box constraint is constructed based on a mixed distribution. Numerical results for some typical scenarios and sensitivity with respect to a priori information are reported to show that the proposed estimator is promising.