Bioinformatics approaches for functional annotation of membrane proteins

Functional classification of membrane transporters and channels based on filtered TM/non-TM amino acid composition

(2012) N. S. Schaadt et al.   BIOPOLYMERS

Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

(2012) Zhenyan Miao et al.   BMC GENOMICS

Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine

(2012) Wei Chen et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Oligomerization of G Protein-Coupled Receptors: Computational Methods

(2012) J. Selent et al.   CURRENT MEDICINAL CHEMISTRY

ABCMdb: A database for the comparative analysis of protein mutations in ABC transporters, and a potential framework for a general application

(2012) Gergely Gyimesi et al.   HUMAN MUTATION

Phylogenetic Characterization of Transport Protein Superfamilies: Superiority of SuperfamilyTree Programs over Those Based on Multiple Alignments

(2012) Jonathan S. Chen et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications

(2012) Cheng-Tsung Lu et al.   NUCLEIC ACIDS RESEARCH

Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties

(2011) Shu-An Chen et al.   BIOINFORMATICS

Bioinformatic approaches for the structure and function of membrane proteins

(2011) Hyun-Jun Nam et al.   BMB Reports

Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins

(2011) Kenichiro Imai et al.   BMC GENOMICS

Comparative Modeling: The State of the Art and Protein Drug Target Structure Prediction

(2011) Tianyun Liu et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Multidrug Resistance ABC Transporter Structure Predictions by Homology Modeling Approaches

(2011) Mylene Honorat et al.   CURRENT DRUG METABOLISM

Computational design of membrane proteins

(2011) Alessandro Senes   CURRENT OPINION IN STRUCTURAL BIOLOGY

Topology Prediction of Helical Transmembrane Proteins: How Far Have We Reached?

(2011) Gabor E. Tusnady et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

An Introduction to Membrane Proteins†

(2011) Linnea E. Hedin et al.   JOURNAL OF PROTEOME RESEARCH

MIPModDB: a central resource for the superfamily of major intrinsic proteins

(2011) A. B. Gupta et al.   NUCLEIC ACIDS RESEARCH

Predicting P-Glycoprotein-Mediated Drug Transport Based On Support Vector Machine and Three-Dimensional Crystal Structure of P-glycoprotein

(2011) Zsolt Bikadi et al.   PLoS One

TSdb: A database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates

(2011) Min Zhao et al.   Science China-Life Sciences

MEDELLER: homology-based coordinate generation for membrane proteins

(2010) Sebastian Kelm et al.   BIOINFORMATICS

Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

(2010) Annalisa Marsico et al.   BMC BIOINFORMATICS

Protein folding in membranes

(2010) Sebastian Fiedler et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Classifying Substrate Specificities of Membrane Transporters fromArabidopsis thaliana

(2010) Nadine S. Schaadt et al.   Journal of Chemical Information and Modeling

Predicting ion channels and their types by the dipeptide mode of pseudo amino acid composition

(2010) Hao Lin et al.   JOURNAL OF THEORETICAL BIOLOGY

GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions

(2010) Xuan Xiao et al.   Molecular BioSystems

The treacherous scent of a human

(2010) Walter S. Leal   NATURE

Odorant reception in the malaria mosquito Anopheles gambiae

(2010) Allison F. Carey et al.   NATURE

VKCDB: voltage-gated K+ channel database updated and upgraded

(2010) W. J. Gallin et al.   NUCLEIC ACIDS RESEARCH

Ion channels: Growing evidence for the role in disease

(2010) Jin Han et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

FoldGPCR: Structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A

(2010) Mayako Michino et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques

(2010) V. P. Satagopam et al.   Database-The Journal of Biological Databases and Curation

GATMD:  -Aminobutyric Acid Transporter Mutagenesis Database

(2010) C. M. Anderson et al.   Database-The Journal of Biological Databases and Curation

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins

(2009) R. Oliva et al.   BIOINFORMATICS

TransportTP: A two-phase classification approach for membrane transporter prediction and characterization

(2009) Haiquan Li et al.   BMC BIOINFORMATICS

Computational Biology of Olfactory Receptors

(2009) Chiquito Crasto   Current Bioinformatics

Predict potential drug targets from the ion channel proteins based on SVM

(2009) Chen Huang et al.   JOURNAL OF THEORETICAL BIOLOGY

SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters

(2009) P.-H. Lee et al.   NUCLEIC ACIDS RESEARCH

MeMotif: a database of linear motifs in α-helical transmembrane proteins

(2009) Annalisa Marsico et al.   NUCLEIC ACIDS RESEARCH

Binding site of ABC transporter homology models confirmed by ABCB1 crystal structure

(2009) Aina W Ravna et al.   Theoretical Biology and Medical Modelling

A nearest neighbor approach for automated transporter prediction and categorization from protein sequences

(2008) H. Li et al.   BIOINFORMATICS

Functional discrimination of membrane proteins using machine learning techniques

(2008) M Michael Gromiha et al.   BMC BIOINFORMATICS

Mitochondrial β-Barrel Proteins, an Exclusive Club?

(2008) Kenichiro Imai et al.   CELL

Dissecting Membrane Insertion of Mitochondrial β-Barrel Proteins

(2008) Stephan Kutik et al.   CELL

MolAxis: a server for identification of channels in macromolecules

(2008) Eitan Yaffe et al.   NUCLEIC ACIDS RESEARCH

TMFunction: database for functional residues in membrane proteins

(2008) M. M. Gromiha et al.   NUCLEIC ACIDS RESEARCH

The Transporter Classification Database: recent advances

(2008) M. H. Saier et al.   NUCLEIC ACIDS RESEARCH