README text for Visusiri Patranavik Potassium Channel models.
MSc Bioinformatics Short Project 2008

sequences modelled were:
rat Kv1.4 (CAA34133 id at NCBI)
Human TASK-1 (O14649 id at NCBI)

template structure:
2r9r (Kv1.2) at RCSB/PDB

method:
in-house (Warwicker lab) program comp_modeller:
sidechain replacement according to mean-field theory
mainchain is not moved

sequence alignment:
clustal (Kv1.2 - Kv 1.4)
following Shealy et al TM and loop alignments for poorl aligning (KV1.2 - TASK-1)
nb only a part of TASK-1 (the pore domain) matches to the KV1.2 template