Can correct protein models be identified?
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Summary
ProQ is developed, a neural‐network‐based method to predict the quality of a protein model that extracts structural features, such as frequency of atom–atom contacts, and predicts thequality of a model, as measured either by LGscore or MaxSub, and shows that ProQ performs at least as well as other measures when identifying the native structure and is better at the detection of correct models.
- Type
- article
- Published
- 2003-05-01
- Cited by
- 761
- References
- 89
- Access
- Open access
- OpenAlex
- https://openalex.org/W1965517743
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:18091323
Keywords
Protein structure prediction, Similarity (geometry), Structural similarity, Function (biology), Protein structure
References
- Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.
- LiveBench‐1: Continuous benchmarking of protein structure prediction servers
- Statistical potentials for fold assessment
- Design of an optimal Chebyshev‐expanded discrimination function for globular proteins
- Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.
- The endless search for primality
- Perspectives in protein-fold recognition.
- Prediction of functionally important residues based solely on the computed energetics of protein structure.
- Accurate modeling of protein conformation by automatic segment matching.
- Protein threading by learning
- Hybrid fold recognition: combining sequence derived properties with evolutionary information.
- A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS
- Information‐theoretic dissection of pairwise contact potentials
- VERIFY3D: assessment of protein models with three-dimensional profiles.
- Ab initio protein structure prediction of CASP III targets using ROSETTA
- Mutational investigation of the specificity determining region of the Src SH2 domain.
- Criteria that discriminate between native proteins and incorrectly folded models
- Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
- FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.
- The interpretation of protein structures: estimation of static accessibility.
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