Procheck checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.

ProSA provides an easy-to-use interface to the program ProSA (Sippl 1993) which is frequently employed in protein structure validation as recognition of errors in experimental and theoretical models of protein structures is a major problem in structural biology.

ERRAT is a protein structure verification algorithm that is especially well-suited for evaluating the progress of crystallographic model building and refinement. The program works by analyzing the statistics of non-bonded interactions between different atom types.

Verify3D analyzes the compatibility of an atomic model (3D) with its own amino acid sequence (1D). Each residue is assigned a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar, etc).

dDFire is an all-atom statistical potential based on a distance-scaled finite ideal-gas reference state. DFIRE is used to assess non-bonded atomic interactions in the protein model.

Naccess is a protein structure verification algorithm that is especially well-suited for evaluating the progress of crystallographic model building and refinement. The program works by analyzing the statistics of non-bonded interactions between different atom types.

MolProbity is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules and can calculate and display the H-bond and van der Waals contacts in the interfaces between components.

D2NReliability of modeled protein structures has emerged as one of the biggest concerns in protein structure prediction (PSP) research. D2N is a distance metric created out of four physico-chemical parameters for predicting RMSD of a modeled protein structure in the absence of a knowledge of its native form. Currently, D2N also calculates TM and GDT scores to assess the quality of the modeled input structure. .