Fast and Accurate Side-Chain Topology and Energy Refinement (FASTER) as a new method for protein structure optimization

Proteins: Structure, Function and Genetics

Volumn 48, Issue 1, 2002, Pages 31-43

  Desmet, Johan ^a   Spriet, Jan ^b   Lasters, Ignace ^a  

^a Algonomics   (Belgium)

^b UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

Combinatorial problem; Dead end elimination; Local minima; Side chain conformation; Side chain flexibility; Structure prediction

Indexed keywords

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; COMBINATORIAL CHEMISTRY; CONFORMATIONAL TRANSITION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THEORY;

ALGORITHMS; AMINO ACIDS; ANIMALS; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SENSITIVITY AND SPECIFICITY; TIME FACTORS;

EID: 0036643430     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10131     Document Type: Article

References (40)

1. Modeling side-chain conformation
2. Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model
3. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design
4. The dead-end elimination theorem and its use in protein sidechain positioning
5. Efficient rotamer elimination applied to protein side-chains and related spin glasses
6. Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side-chains
7. Theoretical and algorithmical optimization of the dead-end elimination theorem
8. * algorithm
9. Conformational splitting: A more powerful criterion for dead-end elimination
10. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: Implications for protein design and structural genomics
11. Computer search algorithms in protein modification and design
12. Protein folding, spin glass and computational complexity
13. De novo protein design: Fully automated sequence selection
14. Automatic protein design with all atom force-fields by exact and heuristic optimization
15. Ab initio loop modeling and its application to homology modeling
16. Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods
17. Computation of the binding of fully flexible peptides to proteins with flexible side chains
18. Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement
19. A method to configure protein side-chains from the main-chain trace in homology modeling
20. Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core
21. Fast and simple Monte Carlo algorithm for side-chain optimization in proteins: Application to model building by homology
22. Optimal sequence selection in proteins of known structure by simulated evolution
23. Prediction and evaluation of side-chain conformations for protein backbone structures
24. A new approach to the rapid determination of protein side chain conformations
25. Genetic algorithms for protein structure prediction
26. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
27. Predicting protein mutant energetics by self-consistent ensemble optimization
28. Conformational analysis of the backbone-dependent rotamer preferences of protein side-chains
29. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
30. Extending the limits of prediction for side-chain conformations
31. Energy functions for protein design
32. All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination
33. Branch- and-terminate: A combinatorial optimization algorithm for protein design
34. Determinants of side chain conformational preferences in protein structures
35. Interactive computer animation of macromolecules
36. CHARMM. A program for macromolecular energy, minimization and dynamics calculations
37. Protein sidechain conformer prediction: A test of the energy function
38. Effective energy functions for protein structure prediction