We develop an efficient and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the regularization technique of Chen, Holst, and Xu; this technique made possible the first a priori pointwise estimates and the first complete solution and approximation theory for the Poisson-Boltzmann equation. It also made possible the first provably convergent discretization of the PBE, and allowed for the development of a provably convergent AFEM for the PBE. However, in practice the regularization turns out to be numerically ill-conditioned. In this article, we examine a second regularization, and establish a number of basic results to ensure that the new approach produces the same mathematical advantages of the original regularization, without the ill-conditioning property. We then design an AFEM scheme based on the new regularized problem, and show that the resulting AFEM scheme is accurate and reliable, by proving a contraction result for the error. This result, which is one of the first results of this type for nonlinear elliptic problems, is based on using continuous and discrete a priori pointwise estimates to establish quasi-orthogonality. To provide a high-quality geometric model as input to the AFEM algorithm, we also describe a class of feature-preserving adaptive mesh generation algorithms designed specifically for constructing meshes of biomolecular structures, based on the intrinsic local structure tensor of the molecular surface. The stability advantages of the new regularization are demonstrated using an FETK-based implementation, through comparisons with the original regularization approach for a model problem. The convergence and accuracy of the overall AFEM algorithm is also illustrated by numerical approximation of electrostatic solvation energy for an insulin protein.