Resources

For Membrane Proteins:

Databases:

• CGDB        - coarse-grained MD models (both helical and barrels)
• HOMEP       - families of homology MP structures
• PDBTM       - all MPs from the PDB, has membrane thickness, updated weekly 
• OPM         - Orientations of Proteins in Membranes with thickness
• MeMotif     - motifs in helical MPs
• TOPDB       - topology database

Alignments:

• PRALINE     - multiple sequence alignment that can use topology info 
• MP-T        - sequence-structure alignments

Secondary structure / TM spans / topology / lipophilicity:

• BCL::Jufo9D - combined secondary structure and TM span prediction
• OCTOPUS     - topology prediction for helical bundles
• BOCTOPUS    - topology prediction for beta-barrels
• LIPS        - prediction of lipophilicity and helix orientation
• TMDET       - membrane regions from 3D structure
• PPM         - membrane regions from 3D structure, server from OPM database

Sequence motifs / interactions:

• PREDDIMER   - predicting 3D structures of dimeric helices
• MemBrain    - prediction of TM helices or inter-helical contacts

Homology modeling:

• Rosetta     - software download
• MODELLER    - software download
• MEDELLER    - server, requires sequence alignment and template structure as input
• MEMOIR      - server, requires sequence and template structure as input
• GoMoDo      - GPCR modeling and docking server

De novo folding:

• EVfold      - uses evolutionary couplings as restraints
• Rosetta     - software download
• BCL::MPFold - software download

Loop modeling:

• FREAD       - fragment assembly from MP loop fragments

Quality assessment:

• ProQM       - discriminates near-native from non-native models
• TMscore     - structural similarity of two protein models