It is designed to be used by structural scientists and researchers reporting and evaluating their data, as well as by educators and students who are seeking to relate structure to function in biological macromolecules. The interface consists of a series of drop-down menus and toolbars and three working areas: folders, comments and palette.
* Adding a limited number of missing heavy atoms to biomolecular structures
* Determining side-chain pKas
* Placing missing hydrogens
* Optimizing the protein for favorable hydrogen bonding
* Assigning charge and radius parameters from a variety of force fields
PEAT Protein Engineering Analysis Tool (PEAT) is a collection of software that aids researchers in the field of protein analysis, engineering and design.
A collection of programs designed for the modeling and analysis of protein structures.
* scap and Sidechain Rotamer library: prediction of side-chain conformations or residue mutations. The operation can be performed on all or certain residues in one or multiple chains.
* loopy + loopyMod: prediction of protein loop conformations or segment mutation. loopyMod used by loopBuilder.
* nest: homology modeling.
PoseView automatically generates high-quality 2D structure-diagrams of protein-ligand complexes provided as 3D-input. Such input may come directly from crystal structures or be computed for example by a docking program.