MAPAS

It’s All About Geometry: Protein Contact Surfaces Hold Key to Cures
Server for protein-membrane contact points is described.


MAPAS Membrane-Associated Protein Assessments
http://cancer-tools.sdsc.edu/MAPAS/pro2.html

protein aggregation

0) http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1828741&blobtype=pdf&tool=pmcentrez
AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides
Aggrescan.

transmembrane proteins

0) http://www.iop.org/EJ/abstract/0953-8984/18/28/S07
Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins
Arguments on using combination of OPLS and united-atom force field in GROMACS.

1) http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm
Explicit Membrane Protein Simulations in NAMD/VMD
Transmembrane protein modeling manual. Human glycophorin (1AFO) made with NAMD software.