MolProbity is a structure-validation web service that provides broad-spectrum solidly based
evaluation of model quality at both the global and local levels for both proteins and nucleic …

The influence of a xenobiotic compound on an organism is usually summarized by the
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …

The small-molecule topology generator PRODRG is described, which takes input from
existing coordinates or various two-dimensional formats and automatically generates …

Continuum solvation models, such as Poisson–Boltzmann and Generalized Born methods,
have become increasingly popular tools for investigating the influence of electrostatics on …

Abstract The Protein Data Bank (PDB) is the world-wide repository of macromolecular
structure information. We present a series of databases that run parallel to the PDB. Each …

Protein preparation is a critical step in molecular simulations that consists of refining a
Protein Data Bank (PDB) structure by assigning titration states and optimizing the hydrogen …

We have developed a computer algorithm, FOLDEF (for FOLD-X energy function), to provide
a fast and quantitative estimation of the importance of the interactions contributing to the …

One of the conclusions drawn at the CASP4 meeting in Asilomar was that applying various
force fields during refinement of template‐based models tends to move predictions in the …

Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their
van der Waals contacts included, was used to choose between the two possible orientations …

With currently more than 126 000 publicly available structures and an increasing growth
rate, the Protein Data Bank constitutes a rich data source for structure-driven research in …