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PLOS COMPUTATIONAL BIOLOGY (2007)
Membrane-protein topology
Gunnar von Heijne
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2006)
Opinion - How many drug targets are there?
John P. Overington et al.
NATURE REVIEWS DRUG DISCOVERY (2006)
Prediction of transmembrane helix orientation in polytopic membrane proteins
Larisa Adamian et al.
BMC STRUCTURAL BIOLOGY (2006)
Towards a proteome-scale map of the human protein-protein interaction network
JF Rual et al.
NATURE (2005)
A human protein-protein interaction network:: A resource for annotating the proteome
U Stelzl et al.
CELL (2005)
An HMM posterior decoder for sequence feature prediction that includes homology information
L Käll et al.
BIOINFORMATICS (2005)
TMDET:: web server for detecting transmembrane regions of proteins by using their 3D coordinates
GE Tusnády et al.
BIOINFORMATICS (2005)
Prediction of membrane protein types by incorporating amphipathic effects
KC Chou et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2005)
How lipids and proteins interact in a membrane: a molecular approach
AG Lee
MOLECULAR BIOSYSTEMS (2005)
SLLE for predicting membrane protein types
M Wang et al.
JOURNAL OF THEORETICAL BIOLOGY (2005)
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank
GE Tusnady et al.
NUCLEIC ACIDS RESEARCH (2005)
A combined transmembrane topology and signal peptide prediction method
L Käll et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Analysing protein-protein interactions with the yeast two-hybrid system
B Causier et al.
PLANT MOLECULAR BIOLOGY (2002)
The HMMTOP transmembrane topology prediction server
GE Tusnády et al.
BIOINFORMATICS (2001)
Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins
L Adamian et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
A Krogh et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Ion channels-related diseases
B Dworakowska et al.
ACTA BIOCHIMICA POLONICA (2000)