Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design

Journal of Molecular Biology

Volumn 299, Issue 3, 2000, Pages 789-803

  Voigt, Christopher A ^a   Gordon, D Benjamin ^b   Mayo, Stephen L ^c  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b California Institute of Technology   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Combinatorial optimization; Protein design

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER AIDED DESIGN; CONFORMATION; INTERMETHOD COMPARISON; PRIORITY JOURNAL; QUANTITATIVE DIAGNOSIS; SEQUENCE ANALYSIS; STOCHASTIC MODEL;

EID: 0034625322     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3758     Document Type: Article

References (49)

1. The Protein Data Bank: A computer-based archival file for macromolecular structures
2. Sequence space, folding and protein design
3. Protein design automation
4. De novo protein design: Fully automated sequence selection
5. Probing the role of packing specificity in protein design
6. Automated design of the surface positions of protein helices
7. De novo protein design: Towards fully automated sequence selection
8. All in one: A highly detailed rotamer library improves both accuracy and speed in the modelling of side-chains by dead-end elimination
9. Computer search algorithms in protein modification and design
10. De novo design of the hydrophobic cores of proteins
11. The dead-end elimination theorem and its use in protein side-chain positioning
12. The dead-end elimination theorem: A new approach to the side-chain packing problem
13. Backbone-dependent rotomer library, for proteins - Application to side-chain prediction
14. Conformational analysis of the backbone-dependent rotamer preferences of protein side-chains
15. In search of the ideal protein sequence
16. Efficient rotamer elimination applied to protein side-chains and related spin glasses
17. Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem
18. Branch-and-Terminate: A combinatorial optimization algorithm for protein design
19. Energy functions for protein design
20. High-resolution protein design with backbone freedom
21. Optimal sequence selection in proteins of known structure by simulated evolution
22. Fast and simple Monte Carlo algorithm for side-chain optimization in proteins: Application to model building by homology
23. De novo protein design using pair-wise potentials and a genetic algorithm
24. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
25. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling
26. Mean-field minimization methods for biological macromolecules
27. Prediction of protein side-chain conformations from local three-dimensional homology relationships
28. De novo design of the hydrophobic core of ubiquitin
29. Predicting protein mutant energetics by self-consistent ensemble optimization
30. Testing homology modeling on mutant proteins: Predicting structural and thermodynamic effects in the Ala98 → Val mutants of T4 lysozyme
31. Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core
32. Prediction of protein side-chain conformation by packing optimization
33. Design, structure and stability of a hyperthermophilic protein variant
34. DREIDING: A generic force-field for molecular simulations
35. Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction
36. Equations of state calculations by fast computing machines
37. Genetic algorithms for protein structure prediction
38. Conformational splitting: A more powerful criterion for dead-end elimination
39. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
40. Comparative protein structure modeling as an optimization problem
41. Conformation, energy, and folding stabilityn of selected amino acid sequences
42. Prediction of homologous protein structures based on conformational searches and energetics
43. Pairwise calculation of protein solvent-accessible surface areas
44. Computational protein design
45. Coupling backbone flexibility and amino acid sequence selection in protein design
46. A new approach to the rapid determination of protein side-chain conformations
47. An evaluation of discrete and continuum search techniques for conformational analysis of side-chains in proteins