ModPipe

ModPipe is a completely automated software pipeline that can calculate protein structure models for a large number of sequences with almost no manual intervention. In the simplest case, it takes as input a sequence identifier and a configuration file and produces one or more comparative models for that sequence.

• Introduction
  • Getting ModPipe
  • ModPipe methodology
  • ModPipe filesystem or directory hierarchy
  • The ModPipe source and its components

• Running ModPipe
  • Overview
  • Examples

• The ModPipe configuration file

• Fold assignment methods
  • Sequence-Sequence search
  • Profile-Sequence search
  • Profile-Profile search
  • Sequence-Profile search

• Developing ModPipe

• Using ModPipe from your own programs

Reference:

• Python modules

Appendices:

• File formats
  • Hits file
  • Models file

• The ModWeb web interface

• Importing data into ModBase

• Installing external programs
  • Modeller
  • BLAST
  • CD-HIT
  • PROCHECK

• Databases used by ModPipe
  • Template sequence database (PDB95)
  • PDB repository
  • Sequence database
  • Structure profiles database

• Copyright and license
  • Embedded licenses

Indices and tables

• Index
• Search Page