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
• ModPipe command line tools
  • Common options
  • modpipe add
  • modpipe build
  • modpipe gather
  • modpipe benchmark
  • modpipe convert
• 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
  • HH-suite
  • CD-HIT
  • PROCHECK
• Databases used by ModPipe
  • Template sequence database (PDB95)
  • PDB repository
  • Sequence database
  • Structure profiles database
• Copyright and license
  • Embedded licenses
• ModPipe change history
  • ModPipe 2.3.1 10-27-2023
  • ModPipe 2.3.0 05-14-2020
  • ModPipe 2.2.0 11-01-2010
  • ModPipe 2.1.3 06-03-2009
  • ModPipe 2.1.2 04-06-2009
  • ModPipe 2.1.1 03-31-2009
  • ModPipe 2.1.0 02-23-2009
  • ModPipe 2.0.2 12-09-2008
  • ModPipe 2.0.1 12-05-2008
  • ModPipe 2.0 10-09-2008

Indices and tables

• Index

• Search Page