Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures.
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Summary
A set of self-consistent potential functions to identify and correct unfavorable Asn/Gln amide rotamers are derived from a database of high-resolution protein crystal structures.
- Type
- article
- Published
- 2006-06-01
- Cited by
- 29
- References
- 30
- Access
- Open access
- OpenAlex
- https://openalex.org/W2083965528
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:42972184
Keywords
Conformational isomerism, Asparagine, Protein structure, Protein Data Bank (RCSB PDB), Chemistry
References
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- The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains.
- Structural and Functional Roles of Asparagine 175 in the Cysteine Protease Papain (*)
- Structural basis for oligosaccharide recognition by Pyrococcus furiosus maltodextrin-binding protein.
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- Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics
- New domain motif: the structure of pectate lyase C, a secreted plant virulence factor.
- Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure
- Positioning hydrogen atoms by optimizing hydrogen‐bond networks in protein structures
- Helmholtz free energy of peptide hydrogen bonds in proteins.
- X-ray structures of the maltose-maltodextrin-binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins.
Cited by
- NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
- Operator-assisted harvesting of protein crystals using a universal micromanipulation robot
- A knowledge‐based potential function predicts the specificity and relative binding energy of RNA‐binding proteins
- Modeling of flexible side chains for protein-ligand docking
- A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models
- Metals in protein structures: a review of their principal features
- Statistical potential for assessment and prediction of protein structures
- Biological activity and ligand binding mode to the progesterone receptor of A-homo analogues of progesterone.
- Self-contacts in Asx and Glx residues of high-resolution protein structures: role of local environment and tertiary interactions.
- Fold space unlimited.
- Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT
- Effective Improvement of D-Phenylglycine Aminotransferase Solubility by Protein Crystal Contact Engineering
- Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes
- Detection of unrealistic molecular environments in protein structures based on expected electron densities
- Visualization of unfavorable interactions in protein folds
- Fast automated placement of polar hydrogen atoms in protein-ligand complexes
- Spectral "Fine" Tuning in Fluorescent Proteins: The Case of the GFP-Like Chromophore in the Anionic Protonation State.
- DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles
- Simplified AutoDock force field for hydrated binding sites.
- Effect of Glutaminase Inhibition in Basal-Like Patient-Derived Xenografts Analyzed by Magnetic Resonance Spectroscopy
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