A molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.
Allows checking of the stereochemical quality of a protein structure. PROCHECK is a suite of programs that uses stereochemical considerations alone, both to provide an overall assessment of the stereochemistry of a given structure and to highlight regions that may need further investigation. The software can be useful for the solution of new structures, assessment of existing structures and model building of unknown structures. PROCHECK-NMR is included in the suite and allows analysis of ensembles of protein structures.
Allows automated determination of molecular structures using X-ray crystallography and other methods. PHENIX is a software suite which provides a range of tools for the analysis, validation and manipulation of X-ray diffraction data. The software was developed as a highly-automated system that can arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data.
A tool for experimental structure determinations and modelling studies. ProSA has a large user base and is employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. ProSA is a tool used to check 3D models of proteins structures for potential errors. The web-based version of ProSA encourages structure depositors to validate their structures before they are submitted to Protein Data Bank (PDB) and to use the tool in early stages of structure determination and refinement.
Establishes the compatibility of an atomic protein model with its own amino acid sequence as measured by a 3D profile. VERIFY3D process by assigning a structural class based on the location and environment of each residue position and by comparing the results to good structures. Environments of residues correspond to three parameters: the local secondary structure, the area of the residue that is buried and the fraction of side-chain area covered by polar atoms.
A standalone suite of programs to plot the distribution of residues embedded at a globular protein interior in the Complementarity Plots. The complementarity plot (CP) is based on packing and electrostatics of amino acid residues buried within globular proteins and is a sensitive indicator of the harmony or disharmony of interior residues with regard to short and long range forces sustaining the native fold. As a structure validation tool, it was reported to be effective in detecting erroneous side-chain torsions in obsoleted structures. The application of CP in protein homology modeling and protein design was also demonstrated. The tool was further extended to the validation of Protein-Protein Interfaces (SARAMAint).