Protein Structure and Function: Applications of Bioinformatics Methods - John Rigden 2014

Ab Initio Protein Structure Prediction
Model Selection
Structure-Sequence Compatibility Function

The third group of Structure/172.html">Model quality assessment programs comprises Methods in which the best models are selected not solely based on Energy Functions, but by applying a sequence-structure compatibility criterion between target sequences and model structures. The earliest and still successful approach is the method by Lüthy et al. (1992), who employed a 3D-1D profiling method along with a corresponding scoring function to evaluate structural quality. Later, another approach (Colovos and Yeates 1993) utilized a quadratic error function to describe non-bonded atomic interactions between CC, CN, CO, NN, NO, and OO atoms, revealing fewer atomic clashes in near-native models compared to others. The Verify3D method (Eisenberg et al. 1997) is an enhancement of Lüthy et al.'s approach achieved by averaging individual residue scores over a 21-residue sliding window6. The GenThreader method (Jones 1999) employs neural networks to distinguish between native and non-native structures. GenThreader's input features include pairwise interaction energies, solvation energies, alignment scores, alignment lengths, as well as sequence and structure dimensions. Similarly, neural networks form The basis of the ProQ method (Wallner and Elofsson 2003), which is used to predict the structural quality of protein models. The input features for ProQ include atomic contacts, accessible surface area, protein shape, Secondary structure, alignment scores between models and templates, and the fraction of the protein modeled based on templates. Recently, a consensus program called ModFold (McGuffin 2007) was developed, incorporating ProQ (Wallner and Elofsson 2003), MODCHECK (Pettitt et al. 2005), and ModSSEA. The authors demonstrated that this consensus method outperforms each of its constituent programs individually.

6 As in the original text. In fact, Verify3D is merely a software Implementation of the method by Lüthy et al. — Translator's Note.



Last update: 06/08/2026

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