Let me show every step necessary to convert between the two notations. Your first equation is properly written as
$$\hat{H} \, | \psi \rangle = E\, | \psi \rangle$$
where $\hat{H}$ is an operator, $|\psi \rangle$ is a state vector, and $E$ is a number. Now, both $\hat{H}$ and $|\psi \rangle$ may be expressed in terms of components in a basis. For example, in the position basis, the components of $|\psi \rangle$ form a function, called the wavefunction,
$$\langle x | \psi \rangle = \psi(x).$$
The Hamiltonian is an operator, so in components, it becomes a matrix, with components
$$H_{xy} = \langle x | \hat{H} | y \rangle.$$
Now let's apply this to the first equation. We hit everything on the left with $\langle x |$, and also insert a copy of the identity,
$$1 = \int dy |y \rangle \langle y|$$
on the left-hand side. This gives
$$\int dy\, \langle x | \hat{H} | y \rangle \langle y | \psi \rangle = E \langle x | \psi \rangle.$$
Expanding in components, we have
$$\int dy \, H_{xy} \psi(y) = E \, \psi(x).$$
This is the Schrodinger equation in components. In your specific case, the components are
$$H_{xy} = -\frac{\hbar^2}{2m} \delta''(x-y).$$
That is, the components are the second derivative of a Dirac delta function. Plugging this in and integrating by parts twice, we have
$$- \frac{\hbar^2}{2m} \int dy \, \delta(x-y) \psi''(y) = E\, \psi(x)$$
Performing the integral, we have
$$-\frac{\hbar^2}{2m} \psi''(x) = E \psi(x).$$
Finally, we can write this in the "abstract" notation
$$- \frac{\hbar^2}{2m} \nabla^2 \psi = E \psi$$
which is your second equation. The difference is that the first equation is truly an abstract operator equation, independent of basis. In the second equation, we have separated out $H$ as an operator, but it acts on coefficients, not on the state vectors themselves. As such, this equation only is useful when working in a particular basis, the position basis.
Emilio Pisanty has given a nice (and much shorter) answer. I think it's good to see the full computation a few times, but after that, you really don't want to descend all the way to components like I just did, since component expressions for operators tend to be very ugly.