TY  - JOUR
AU  - Farkas, Bianka Vivien
AU  - Gáspárné Csizmadia, Georgina
AU  - Katona, Eszter
AU  - Tusnády, Gábor
AU  - Hegedűs, Tamás
TI  - MemBlob database and server for identifying transmembrane regions using cryo-EM maps
JF  - BIOINFORMATICS
J2  - BIOINFORMATICS
VL  - 36
PY  - 2020
IS  - 8
SP  - 2595
EP  - 2598
PG  - 4
SN  - 1367-4803
DO  - 10.1093/bioinformatics/btz539
UR  - https://m2.mtmt.hu/api/publication/30745372
ID  - 30745372
N1  - Cited By :2            
            Export Date: 15 May 2020
Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary            
            MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, 1094, Hungary            
            Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, 1083, Hungary            
            Faculty of Brain Sciences, University College London, London, W1T 7NF, United Kingdom            
            'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, 1117, Hungary            
            Cited By :2            
            Export Date: 24 July 2020            
            CODEN: BOINF            
            Correspondence Address: Hegedus, T.; Department of Biophysics and Radiation Biology, Semmelweis UniversityHungary; email: tamas.hegedus@hegelab.org            
            Funding details: HEGEDU18I0            
            Funding details: K127961, K125607, K119287, K111678            
            Funding details: Cystic Fibrosis Foundation            
            Funding text 1: This work was supported by the National Research, Development and Innovation Office [K111678, K119287, K125607, K127961], the Cystic Fibrosis Foundation [CFF HEGEDU18I0] and the Semmelweis Science and Innovation Fund.
AB  - The identification of transmembrane helices in transmembrane proteins is crucial, not only to understand their mechanism of action, but also to develop new therapies. While experimental data on the boundaries of membrane-embedded regions is sparse, this information is present in cryo-electron microscopy (cryo-EM) density maps and it has not been utilized yet for determining membrane regions. We developed a computational pipeline, where the inputs of a cryo-EM map, the corresponding atomistic structure, and the potential bilayer orientation determined by TMDET algorithm of a given protein result in an output defining the residues assigned to the bulk water phase, lipid interface, and the lipid hydrophobic core. Based on this method, we built a database involving published cryo-EM protein structures and a server to be able to compute this data for newly obtained structures.http://memblob.hegelab.org.Supplementary data are available at Bioinformatics online.
LA  - English
DB  - MTMT
ER  - 

TY  - JOUR
AU  - Tusnády, Gábor
AU  - Dosztányi, Zsuzsanna
AU  - Simon, István
TI  - TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates
JF  - BIOINFORMATICS
J2  - BIOINFORMATICS
VL  - 21
PY  - 2005
IS  - 7
SP  - 1276
EP  - 1277
PG  - 2
SN  - 1367-4803
DO  - 10.1093/bioinformatics/bti121
UR  - https://m2.mtmt.hu/api/publication/1011228
ID  - 1011228
AB  - Summary: The structure of integral membrane proteins is determined in the absence of the lipid bilayer; consequently the membrane localization of the protein is usually not specified in the corresponding PDB file. Recently, we have developed a new method called TMDET which determines the most possible localization of the membrane relative to the protein structure, and gives the annotation of the membrane embedded parts of the sequence. The entire Protein Data Bank has been scanned by the new TMDET algorithm resulting in the database of structurally determined transmembrane proteins (PDB_TM). Here we present the web interface of the TMDET algorithm to allow scientists to determine the membrane localization of structural data prior to deposition or to analyze model structures. © The Author 2004. Published by Oxford University Press. All rights reserved.
LA  - English
DB  - MTMT
ER  -