Statistical potentials for fold assessment
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Summary
Four types of a residue‐level statistical potential were optimized, including distance‐dependent, contact, ϕ/Ψ dihedral angle, and accessible surface statistical potentials, providing a basis for an optimal use of Statistical potentials in fold assessment.
- Type
- article
- Published
- 2002-02-01
- Cited by
- 379
- References
- 117
- Access
- Open access
- OpenAlex
- https://openalex.org/W11790853
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:15363613
Keywords
Rheology, Viscoelasticity, Materials science, Rheometer, Dynamic shear rheometer
References
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- A method for the improvement of threading‐based protein models
- A computational approach to simplifying the protein folding alphabet
- Protein structure modeling for structural genomics
- An analysis of incorrectly folded protein models. Implications for structure predictions.
- Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force.
- Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.
- Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.
- Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures.
- Protein folding. Effect of packing density on chain conformation.
- Perspectives in protein-fold recognition.
- Comparative modelling of major house dust mite allergen Der p I: structure validation using an extended environmental amino acid propensity table.
- Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
- Large-scale protein structure modeling of the Saccharomyces cerevisiae genome.
- Comparison of database potentials and molecular mechanics force fields.
- Knowledge-based potentials for proteins.
- Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
- Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
Cited by
- Database-derived potentials dependent on protein size for in silico folding and design.
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- Learning MHC I - peptide binding
- Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
- Extending the PRIME Model for Protein Aggregation to All Twenty Amino Acids
- Application of information theory to feature selection in protein docking
- Multicofactor proteins: structure,prediction, function
- First co-expression of a lipase and its specific foldase obtained by metagenomics
- Allosteric sodium binding cavity in GPR3: a novel player in modulation of Aβ production
- Investigating the antibacterial potency and spectrum of activity of the antibiotic thiomarinol
- Protein structure modeling with MODELLER.
- Macromolecular assembly structures by comparative modeling and electron microscopy.
- Molecular Modelling of Multi-Drug Resistance Transporters
- The Proteomics Protocols Handbook
- Visualising plasmodium falciparum functional genomic data in MaGnET: malaria genome exploration tool
- Algorithms for protein comparative modelling and some evolutionary implications
- Structural and Functional Studies on IroB: A Pathogen-Associated C-glycosyltransferase
- Computational Studies of Benzoxazinone Derivatives as Antiviral Agents against Herpes Virus Type 1 Protease
- Engineering of HIV gp120 by yeast surface display for neutralizing antibody characterization and immunogen design
- Analysis of Porphyromonas gingivalis PG27 by deletion and intragenic suppressor mutation analyses.
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