PDBTM: Protein Data Bank of transmembrane proteins after 8 years

By Dániel Kozma, István Simon, Gábor E. Tusnády. 2012

276 citations recorded by the source corpus.

The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ∼400 to 1700 entries but also new structural elements have been identified, in addition to the well-known α-helical bundle and β-barrel structures. Numerous ‘exotic’ transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community.

Subfields: Molecular Biology

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Citations in the corpus

Folding membrane proteins by deep transfer learning (2017, background): “The most structurally similar proteins in PDB70 found by DeepSearch (Eddy, 2011) for 5h35E are 5egiA and 5eikA, which have TMscore 0.677 and 0.653 with the native structure of this target, respectively.”
Predicting membrane protein contacts from non-membrane proteins by deep transfer learning (2017, background): “Currently there are only about 510 non-redundant MPs with solved structures [2].”
CCTOP: a Consensus Constrained TOPology prediction web server (2015, methodology): “There are two interface types for using CCTOP: a web server with browser friendly GUI written in C++ using the Wt web toolkit programming library along with our in-house developed XBuilder library developed for our previous works (6,49) and an unpretentious PHP based frontend for scripts.”
Ins and outs of AlphaFold2 transmembrane protein structure predictions (2022, methodology): “To support this finding with experimental data, the hydrophobic thickness of experimentally determined human transmembrane protein structures was retrieved from the PDBTM database [17].”
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides (2015, methodology): “For topology assignment, we combined different sources (PDBTM, OPM (35), TOPDB (36) and UniProt), along with manual inspection in some spurious cases.”
An Integrated Framework Advancing Membrane Protein Modeling and Design (2015, methodology): “For the starting structure, we used model 1 of the NMR structure from the PDBTM [15].”
Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4* (2015, methodology): “formed structural alignments between the model and all known crystal structures of membrane proteins, in the Protein Data Bank of Transmembrane Proteins), using TM-align (30, 31, 37).”
Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations (2021, methodology): “Here, the GPCR-EXP, PDBTM, and MPstruct databases are used for determining whether a template belongs to the membrane protein.”
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry (2018, methodology): “Specifically, we filtered all the PDB entries in the PDBTM database (version: 16 June 2017) (40) with the following criteria.”
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP (2016, methodology): “The structures in each set were downloaded from the PDBTM database [26], for which the proteins are already transformed into the membrane coordinate frame: the membrane center is defined as the origin at (x, y, z) = (0, 0, 0) and the membrane normal vector lies along the z-axis with (0, 0, 1).”