A study on protein sequence alignment quality

Proteins: Structure, Function and Genetics

Volumn 46, Issue 3, 2002, Pages 330-339

  Elofsson, Arne ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Dynamic programming; Fold recognition; Hidden Markov models; Homology modeling; Sequence alignment

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; CONFERENCE PAPER; MODEL; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN QUALITY; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

COMPUTATIONAL BIOLOGY; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 0037083541     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10043     Document Type: Conference Paper

References (43)

1. Identification of common molecular subsequences
2. A general method applicable to the search for similarities in the amino acid sequence of two proteins
3. Clustal w: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
4. Profile analysis: Detection of distantly related proteins
5. Gapped blast and psi-blast: A new generation of protein database search programs
6. Protein fold recognition using sequence-derived predictions
7. Protein fold recognition by prediction-based threading
8. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence
9. A new approach to protein fold recognition
10. Large-scale protein structure modeling of the saccharomyces cerevisiae genome
11. Alignment algorithm for homolgy modeling and threading
12. Do aligned sequences share the same fold?
13. Assessing sequence comparison methods with reliable structurally identified evolutionary relationships
14. Intermediate sequences increase the detection of homology between sequences
15. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
16. Fold recognition using predicted secondary structure sequences and hidden Markov models of proteins folds
17. Identification of related proteins on family, superfamily and fold level
18. Better 1d predictions by 'experts' with machines
19. Structure based evaluation of sequence comparison and fold recognition alignment accuracy
20. Combination of threading potentials and sequence profiles improves fold recognition
21. Improving the quality of twilight-zone alignments
22. Large-scale comparison of protein sequence alignment algorithms with structure alignments
23. A study if quality measured for protein threading models
24. A comprehensive comparison of multiple sequence alignment programs
25. Optimum superimposition of protein structures, ambiguities and implications
26. The structural alignment between two proteins. Is there a unique answer?
27. Livebench: Continuous benchmarking of protein structure prediction servers
28. Hidden markov models for detecting remote protein homologies
29. Comparison of sequence profiles. Strategies for structural predictions using sequence information
30. Benchmarking psi-blast in genome annotation
31. Pcons: A neural network based consensus predictor that improves fold recognition
32. A unified statistical framework for sequence comparison and structure comparison
33. Processing and analysis of casp3 protein structure predictions
34. Rmsd/coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions
35. Maxsub: An automated measure to assess the quality of protein structure predictions
36. Scop: A structural classification of proteins database for the investigation of sequences and structures
37. Selection of representative protein data sets
38. Profile hidden markov models
39. Kind-a non-redundant protein database
40. Enhanced genome annotation using structural profiles in the program 3d-pssm