Contents
Preface
List of protocols
Abbreviations
1 Threading methods for protein structure prediction
1 Introduction
2 Threading methods
1-Dβ3-D profiles: Bowie et al. (1991)
Threading: Jones et al. (1992)
Protein fold recognition using secondary structure predictions: Rost (1997)
Combining sequence similarity and threading: Jones (1999)
3 Assessing the reliability of threading methods
Alignment accuracy
Post-processing threading results
Why does threading work?
4 Limitations: strong and weak fold-recognition
The domain problem in threading
5 The future
References
2 Comparison of protein three-dimensional structures
1 Introduction
2 The comparison of protein structures
General considerations
What atoms/features of protein structure to compare?
Standard methods for finding the translation vector and rotation matrix
Standard methods to determine equivalent matched atoms between structures
Quality and extent of structural matches
3 The comparison of identical proteins
Why compare identical proteins?
Comparisons
4 The comparison of homologous structures: example methods
Background
Methods that require the assignment of seed residues
Automatic comparison of 3-D structures
Multiple structural comparisons
5 The comparison of unrelated structures
Background
6 Large-scale comparisons of protein structures
References
3 Multiple alignments for structural, functional, or phylogenetic analyses of homologous sequences
1 Introduction
2 Basic concepts for multiple sequence alignment
Homology: definition and demonstration
Global or local alignments
Substitution matrices, weighting of gaps
3 Searching for homologous sequences
4 Multiple alignment methods
Optimal methods for global multiple alignments
Progressive global alignment
Block-based global alignment
Motif-based local multiple alignments
Comparison of different methods
Particular case: aligning protein-coding DNA sequences
5 Visualizing and editing multiple alignments
Manual expertise to check or refine alignments
Annotating alignments, extracting sub-alignments
Comparison of alignment editors
Alignment shading software, pretty printing, logos, etc.
6 Databases of multiple alignments
7 Summary
References
4 Hidden Markov models for database similarity searches
1 Introduction
2 Overview
3 Using profile and profile-HMM databases
Pfam
Prosite profiles
SMART
Other resources and future directions
Limitations of profile-HMM databases
4 Using PSI-BLAST
5 Using HMMER2
Overview of using HMMER
Making the first alignment
Making a profile-HMM from an alignment
Finding homologues and extending the alignment
6 False positives
7 Validating a profile-HMM match
8 Practical issues of the theories behind profile-HMMs
Overview of profile-HMMs
Statistics for profile-HMM
Profile-HMM construction
Priors and evolutionary information
Technical issues
References
5 Protein family-based methods for homology detection and analysis
1 Introduction
Expanding protein families
Terms used to describe relationships among proteins
Alternative approaches to inferring function from sequence alignment
2 Displaying protein relationships
From pairwise to multiple-sequence alignments
Patterns
Logos
Trees
3 Block-based methods for multiple-sequence alignment
Pairwise alignment-initiated methods
Pattern-initiated methods
Iterative methods
Implementations
4 Position-specific scoring matrices (PSSMs)
Sequence weights
PSSM column scores
5 Searching family databases with sequence queries
Curated family databases: Prosite, Prints, and Pfam
Clustering databases: ProDom, DOMO, Protomap, and Prof_pat
Derived family databases: Blocks and Proclass
Other tools for searching family databases
6 Searching with family-based queries
Searching with embedded queries
Searching with PSSMs
Iterated PSSM searching
Multiple alignment-based searching of protein family databases
References
6 Predicting secondary structure from protein sequences
1 Introduction
What is secondary structure?
Where could knowledge about secondary structure help?
What signals are there to be recognized?
2 Assessing prediction accuracy
3 Prediction methods for globular proteins
The early methods
Accuracy of early methods
Other computational approaches
Prediction from multiply-aligned sequences
A consensus approach: JPRED
Multiple-alignment quality and secondary-structure prediction
Iterated multiple-alignment and secondary structure prediction
4 Prediction of transmembrane segments
Prediction of .-helical TM segments
Orientation of transmembrane helices
Prediction of .-strand transmembrane regions
5 Coiled-coil structures
6 Threading
7 Recommendations and conclusions
References
7 Methods for discovering conserved patterns in protein sequences and structures
1 Introduction
2 Pattern descriptions
Exact or approximate matching
PROSITE patterns
Alignments, profiles, and hidden Markov models
Pattern significance
Pattern databases
Using existing pattern collections
3 Finding new patterns
A general approach
Discovery algorithms
4 The Pratt programs
Using Pratt
Pratt: Internal search methods
Scoring patterns
5 Structure motifs
The SPratt program
6 Examples
7 Conclusions
References
8 Comparison of protein sequences and practical database searching
1 Introduction
2 Alignment of sequences
Rigorous alignment algorithms
Heuristic algorithms for sequence comparison
3 Probability and statistics of sequence alignments
Statistics of global alignment
Statistics of local alignment without gaps
Statistics of local alignment with gaps
4 Practical database searching
Types of comparison
Databases
Algorithms
Filtering
Scoring matrices and gap penalties
Command line parameters
5 Interpretation of results
6 Conclusion
References
9 Networking for the biologist
1 Introduction
2 The changing face of networking
Networking in Europe
The way we were ... e-mail servers for sequence retrieval
Similarity searches via e-mail
Speed solutions for similarity searches
3 Sequence retrieval via the WWW
Entrez from the NCBI
SRS from the EBI
4 Submitting sequences
Bankit at NCBI
Sequin from NCBI
Webin from EBI
Sakura from DDJB
5 Conclusions
References
10 SRSβAccess to molecular biological databanks and Integrated data analysis tools
1 Introduction
SRS fills a critical need
History, philosophy, and future of SRS
2 A user's primer
A simple query
Exploiting links between databases
Using Views to explore query results
Launching analysis tools
Overview
3 Advanced tools and concepts
Refining queries
Creating custom Views
SRS world wide: using DATABANKS
Interfacing with SRS over the network
4 SRS server side
User's point of view
Administrator's point of view
5 Where to turn to for help
Acknowledgements
References
List of suppliers
Index
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