While learning THREE.js, I coded an online app to sculpt with vertices.
Site URL: http://www.pleek.net/vertexlove/
Vertex Love is a playground for coding GLSL Vertex shaders.
Given a box filled with vertices/points, you can sculpt, warp, deform and color this cube into something completely different by coding the shader within the editor.
All the vertices lie inside a normalized space of 1.0 x 1.0 x 1.0 units.
You are also given 3 sliders. Their value gets input into the shader, so you can easily test and manipulate the visuals.
You can rotate and zoom the view.
Happy vertex sculpting!