Ab initio construction of protein tertiary structures using a hierarchical approach

Journal of Molecular Biology

Volumn 300, Issue 1, 2000, Pages 171-185

  Xia, Yu ^a   Huang, Enoch S ^b   Levitt, Michael ^a   Samudrala, Ram ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Cereon Genomics   (United States)

Author keywords

Decoy approach; Discriminatory function; Knowledge based; Lattice model; Protein structure prediction

Indexed keywords

M PROTEIN;

ARTICLE; ENERGY; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN LOCALIZATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

EID: 0034733381     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3835     Document Type: Article

References (45)

1. Principles that govern the folding of protein chains
2. The Protein Data Bank: A computer-based archival file for macromolecular structures
3. A combinatorial distance-constraint approach to predicting protein tertiary models from known secondary structure
4. On the prediction of protein structure: The significance of root-mean-square deviation
5. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
6. Prediction of protein tertiary structure to low resolution: Performance for a large and structurally diverse test set
7. Knowledge-based secondary structure assignment
8. New Monte Carlo algorithms for protein folding
9. A lattice model for protein structure prediction at low resolution
10. Exploring conformational space with a simple lattice model for protein structure
11. Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures
12. Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions
13. SCOP: A structural classification of proteins database
14. Protein secondary structure prediction based on position-specific scoring matrices
15. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
16. A brighter future for protein structure prediction
17. Effective energy function for proteins in solution
18. Calculation of protein conformation by global optimization of a potential energy function
19. Are there pathways for protein folding?
20. Energy refinement of hen egg-white lysozyme
21. Refinement of protein conformations using a macromolecular energy minimization procedure
22. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
23. Prediction of protein structure: The problem of fold multiplicity
24. Test for comparing related amino acid sequences
25. Comparison of database potentials and molecular mechanics force fields
26. Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction
27. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments
28. Ab initio folding of proteins using restraints derived from evolutionary information
29. Improved ab initio predictions with a simplified, flexible geometry model
30. The complexity and accuracy of discrete state models of protein structure
31. Energy functions that discriminate X-ray and near native folds from well-constructed decoys
32. Factors affecting the ability of energy functions to discriminate correct from incorrect folds
33. Genetic algorithms for protein structure prediction
34. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction
35. PHD - An automatic mail server for protein secondary structure prediction
36. An all-atom distance dependent conditional probability discriminatory function for protein structure prediction
37. Ab initio protein structure prediction using a combined hierarchical approach
38. Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches
39. Constructing side-chains on near-native main-chains for ab initio protein structure prediction
40. Recent developments in the theory of protein folding: Searching for the global energy minimum
41. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions
42. Ab initio protein structure prediction of CASP III targets using ROSETTA
43. Validation of molecular dynamics simulation
44. Are predicted structures good enough to preserve functional sites?