A multiscale theoretical and computational methodology will be presented for studying biomolecular systems across multiple length and time scales. The approach provides a systematic connection between all-atom molecular dynamics, coarse-grained modeling, and mesoscopic phenomena. At the heart of the approach is the multiscale coarse-graining method for rigorously deriving coarse-grained models from the underlying molecular-scale interactions. Applications of the multiscale approach will be given for membranes and proteins, although the overall methodology is applicable to many other complex condensed matter systems. Recent applications to large protein complexes will also be described. The computational challenges and opportunities for this area of molecular modeling will be especially emphasized.