Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.
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Summary
This work presents a method for rapidly predicting the conformations of protein side-chains, starting from main-chain coordinates alone, and results compared favorably with existing methods over a comprehensive data set.
- Type
- article
- Published
- 1997-04-18
- Cited by
- 560
- References
- 60
- OpenAlex
- https://openalex.org/W2013238066
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:4143766
Keywords
Conformational isomerism, Dihedral angle, Side chain, Steric effects, Homology (biology)
References
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- Principles of Protein Structure
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- Analysis of the relationship between side-chain conformation and secondary structure in globular proteins.
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- A new approach to the rapid determination of protein side chain conformations.
- Variability of conformations at crystal contacts in BPTI represent true low‐energy structures: Correspondence among lattice packing and molecular dynamics structures
- A critical comparison of search algorithms applied to the optimization of protein side‐chain conformations
Cited by
- Visualisation of bioinformatics datasets
- Homology modeling and substrate binding study of human CYP2C18 and CYP2C19 enzymes
- Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure.
- On the role of the crystal environment in determining protein side-chain conformations.
- De novo design of foldable proteins with smooth folding funnel: automated negative design and experimental verification.
- COLORADO3D, a web server for the visual analysis of protein structures
- Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing
- Effects on Ligand Interaction and Membrane Translocation of the Positively Charged Arginine Residues Situated along the C1 Domain Binding Cleft in the Atypical Protein Kinase C Isoforms*
- IRECS: A new algorithm for the selection of most probable ensembles of side‐chain conformations in protein models
- The role of protein 3D-structures in the drug discovery process.
- Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation
- Structure of Ca2+ release channel at 14 A resolution.
- Protein side chain conformation predictions with an MMGBSA energy function
- ORGANIZING FORCES AND CONFORMATIONAL ACCESSIBILITY IN THE UNFOLDED STATE OF PROTEINS
- Valine 77 of heterocystous ferredoxin FdxH2 in Anabaena variabilis strain ATCC 29413 is critical for its oxygen sensitivity
- Engineering high performance variants of Bacillusthermolysin-like proteases
- Prediction of structure, function, and spectroscopic properties of G-protein-coupled receptors : methods and applications.
- Rotamer-specific Statistical Potentials for Protein Structure Modeling.
- Protein structure prediction and analysis as a tool for functional genomics.
- Combining Empirical and Experimental Data in Protein Structure Determination
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