Since the introduction of programmable Graphics Processing Units (GPUs) and procedural shaders, hardware vendors have each developed their own individual real-time shading language standard. None of these shading languages is fully platform independent. Although this real-time programmable shader technology could be developed into 3D application on a single system, this platform dependent limitation keeps the shader technology away from 3D Internet applications. The primary purpose of this dissertation is to design a framework for translating different shader formats to platform independent shaders and embed them into the eXtensible 3D (X3D) scene for 3D web applications. This framework includes a back-end core shader converter, which translates shaders among different shading languages with a middle XML layer. Also included is a shader library containing a basic set of shaders that developers can load and add shaders to. This framework will then be applied to some applications in Biomolecular Visualization.