Contents
Release 2005, March 2005
1. Introduction
- What is SeqFold?
- Invoking SeqFold
- Running SeqFold
- Seqfold standalone
- A note about implementation
2. Theory
- Predicting protein structure and function
- Threading algorithms
- SeqFold scoring function
- SeqFold alignment method
- MultiView: multiple features analysis
3. Methodology
- Introduction
- Typical steps
- Using the default parameters
- Changing the default parameter values
4. Tutorial
- Leptin hormone fold recognition
- Phosphatidylethanolamine binding protein
5. Command Summary
- Fold_Search
- Parameters
- Fold_Browse
- Fold_Load
- Manage_Profiles
A. References
B. File formats
- pseq file format
- 1d_prf file format
- Accelrys sequence similarity matrix file format
- NCBI sequence similarity matrix file format
- General sequence similarity matrix file format
- inf file format
C. Parameter Key
- Absolute
- Relative
D. DSC (Discrimination of protein Secondary structure Class)
- Disclaimer
- Introduction
- Input/Output
- Basic I/O options
- Smoothing options
- Removing regions of poor alignment
- Miscellaneous options
- Methods
- Residue propensities and GOR
- Other residue based concepts in prediction
- Information from aligned sequences
- Attribute vectors
- Linear discrimination
- Post processing
- References
Last updated November 22, 2003.
Copyright © 2003, Accelrys Inc. All rights
reserved.