We consider a broad class of systems of nonlinear integro-differential equations posed on the real line that arise as Euler-Lagrange equations to energies involving nonlinear nonlocal interactions. Although these equations are not readily cast as dynamical systems, we develop a calculus that yields a natural Hamiltonian formalism. In particular, we formulate Noether's theorem in this context, identify a degenerate symplectic structure, and derive Hamiltonian differential equations on finite-dimensional center manifolds when those exist. Our formalism yields new natural conserved quantities. For Euler-Lagrange equations arising as traveling-wave equations in gradient flows, we identify Lyapunov functions. We provide several applications to pattern-forming systems including neural field and phase separation problems.