Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation

Proteins: Structure, Function and Genetics

Volumn 43, Issue 1, 2001, Pages 1-11

  Bonneau, Richard ^a   Strauss, Charlie E M ^b   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Ab initio structure prediction; Homology; Rosetta

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CLUSTER ANALYSIS; ENERGY; GENETIC PROCEDURES; HYDROPHOBICITY; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

ALGORITHMS; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 0035314042     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20010401)43:1<1::AID-PROT1012>3.0.CO;2-A     Document Type: Article

References (30)

1. Critical assessment of methods of protein structure prediction (CASP): Round III
2. Some measures of comparative performance in the three CASPs
3. Prediction of protein tertiary structure to low resolution: Performance for a large and structurally diverse test set
4. Factors affecting the ability of energy functions to discriminate correct from incorrect folds
5. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence
6. Knowledge-based potentials for proteins
7. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
8. Do aligned sequences share the same fold?
9. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
10. A structural explanation for the twilight zone of protein sequence homology
11. Database of homology-derived protein structures and the structural meaning of sequence alignment
12. Intermediates and barrier crossing in a random energy model
13. How homologs can help to predict protein folds even though they cannot be predicted for individual sequences
14. Averaging interaction energies over homologs improves protein fold recognition in gapless threading
15. Coupling the folding of homologous proteins
16. Additivity principles in biochemistry
17. Decomposition of the free energy of a system in terms of specific interactions
18. An evolutionary approach to folding small α-helical proteins that uses sequence information and an empirical guiding fitness function
19. Recognizing native folds by the arrangement of hydrophobic and polar residues
20. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
21. Ab initio protein structure prediction of CASP III targets using ROSETTA
22. Clustering of low-energy conformations near the native structures of small proteins
23. The CATH Database provides insights into protein structure/function relationships
24. The HSSP data base of protein structure-sequence alignments
25. Weighting in sequence space: A comparison of methods in terms of generalized sequences
26. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
27. MView: A web-compatible database search or multiple alignment viewer
28. Protein secondary structure prediction based on position-specific scoring matrices
29. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction
30. Prediction of protein secondary structure at better than 70% accuracy