MemBlob database and server for identifying transmembrane regions using cryo-EM maps.
Bioinformatics
; 36(8): 2595-2598, 2020 04 15.
Article
en En
| MEDLINE
| ID: mdl-31290936
ABSTRACT
SUMMARY:
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 are 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. AVAILABILITY AND IMPLEMENTATION http//memblob.hegelab.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Algoritmos
/
Proteínas de la Membrana
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2020
Tipo del documento:
Article
País de afiliación:
Hungria