Methods and systems to apply motion estimation (ME) based on reconstructed reference pictures in a B frame or in a P frame at a video decoder. For a P frame, projective ME may be performed to obtain a motion vector (MV) for a current input block. In a B frame, both projective ME and mirror ME may be performed to obtain an MV for the current input block. The ME process can be performed on sub-partitions of the input block, which may reduce the prediction error without increasing the amount of MV information in the bitstream. Decoder-side ME can be applied for the prediction of existing inter frame coding modes, and traditional ME or the decoder-side ME can be adaptively selected to predict a coding mode based on a rate distribution optimization (RDO) criterion.