A graph‐theory algorithm for rapid protein side‐chain prediction
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Summary
A new algorithm forSCWRL is presented that uses results from graph theory to solve the combinatorial problem encountered in the side‐chain prediction problem, and will allow for use of SCWRL in more demanding applications such as sequence design and ab initio structure prediction, as well addition of a more complex energy function and conformational flexibility, leading to increased accuracy.
- Type
- article
- Published
- 2003-09-01
- Cited by
- 1,080
- References
- 49
- Access
- Open access
- OpenAlex
- https://openalex.org/W2015403140
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:3635723
Keywords
Dihedral angle, Conformational isomerism, Vertex (graph theory), Computer science, Ab initio
References
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Cited by
- Novel Algorithms for Computational Protein Design, with Applications to Enzyme Redesign and Small-Molecule Inhibitor Design
- Multiple methods for protein side chain packing using maximum weight cliques.
- Rapid evolution of cytochrome c oxidase subunit II in camelids (Tylopoda, Camelidae)
- Prediction and simulation of motion in pairs of transmembrane α-helices
- IRECS: A new algorithm for the selection of most probable ensembles of side‐chain conformations in protein models
- FireDock: Fast interaction refinement in molecular docking
- Crystal structure of peanut (Arachis hypogaea) allergen Ara h 5.
- Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design
- Protein Structure Prediction Using CABS – A Consensus Approach
- Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation
- Protein side chain conformation predictions with an MMGBSA energy function
- Characterization of specific allosteric effects of the Na+ channel β1 subunit on the Nav1.4 isoform
- Prédiction de structures de macromolécules par apprentissage automatique
- Structure/function studies of the P2X receptor
- Sparsity regularization and graph-based representation in medical imaging
- Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation.
- Identifying Calcium-Binding Sites and Predicting Disulfide Connectivity
- Peptide synthesis and self-assembly.
- Prédiction structurale et ingénierie des assemblages macromoléculaires par bioinformatique
- Etude par modélisation moléculaire des propriétés mécaniques d'un système membranaire : le canal mécanosensible MscL au sein de bicouches lipidiques modèles. (Mechanical properties of a membrane system studied by molecular dynamics: the mechanosensitive channel MscL in model lipids bilayers)
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