All docking methods employ some sort of heuristic to orient the ligand molecules into the
binding site of the target structure. An automated method, MCSS2SPTS, for generating …

Background Many proteins undergo extensive conformational changes as part of their
functionality. Tracing these changes is important for understanding the way these proteins …

The conformer generator ETKDG is a stochastic search method that utilizes distance
geometry together with knowledge derived from experimental crystal structures. It has been …

Several modifications and additions to Fitted1. 5 led to the development of Fitted2. 6. Among
the novel implementations are a matching algorithm-enhanced genetic algorithm and a ring …

A unifying principle of rational drug design is the use of either shape similarity or
complementarity to identify compounds expected to be active against a given target. Shape …

We present here a greatly updated version of an earlier study on the conformational
energies of protein–ligand complexes in the Protein Data Bank (PDB)[Nicklaus et al. Bioorg …

Sampling alternative conformations is key to understanding how proteins work and
engineering them for new functions. However, accurately characterizing and modeling …

Prediction of protein loop conformations without any prior knowledge (ab initio prediction) is
an unsolved problem. Its solution will significantly impact protein homology and template …

Molecular modeling methodologies such as molecular docking, pharmacophore modeling,
and 3D-QSAR, rely on conformational searches of small molecules as a starting point. All of …

Quantifying the relative energy of a ligand in its target‐bound state (ie the bioactive
conformation) is essential to understand the process of molecular recognition, to optimize …