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PDBTM specifications

Information


Unique identifier OMICS_01613
Name PDBTM
Alternative name Protein Data Bank of Transmembrane Proteins
Restrictions to use None
Data access Browse
Maintained No

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Publications for Protein Data Bank of Transmembrane Proteins

PDBTM citations

 (25)
library_books

Statistically derived asymmetric membrane potentials from α helical and β barrel membrane proteins

2018
Sci Rep
PMCID: 5849751
PMID: 29535329
DOI: 10.1038/s41598-018-22476-6

[…] ntists have thus derived scoring functions to predict protein embedding in the membrane; however, lack of benchmarking data precludes extensive testing of these methods. An earlier method used by the PDBTM database is TMDET, which cuts the protein into slices and uses hydrophobicity and structural information of the Cα-trace (such as straightness, turns, and termini) to derive an objective functio […]

library_books

Molecular Properties of Globin Channels and Pores: Role of Cholesterol in Ligand Binding and Movement

2016
Front Physiol
PMCID: 5011150
PMID: 27656147
DOI: 10.3389/fphys.2016.00360

[…] dition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB, and TODOM data bases using the probabilistic framework of hidden Markov model (Dobson et al., ).Based on X-ray crystallography data (PDB files), Pellegrini-Calace et al. () have develope […]

library_books

Membrane Proteins Are Dramatically Less Conserved than Water Soluble Proteins across the Tree of Life

2016
Mol Biol Evol
PMCID: 5062322
PMID: 27501943
DOI: 10.1093/molbev/msw164

[…] omputed in the same manner for and supplementary figure S3, Supplementary Material online.For results in , the entire nonredundant set of PDB amino-acid sequences and annotations was downloaded from pdbtm.enzim.hu (). This data set is constantly updated to include all PDB structures for membrane proteins in the PDB database, and the files parsed into annotations for the subcellular localization o […]

call_split

Characterization of Disease Associated Mutations in Human Transmembrane Proteins

2016
PLoS One
PMCID: 4795776
PMID: 26986070
DOI: 10.1371/journal.pone.0151760
call_split See protocol

[…] e 3D structures of TMPs; the membrane normal was parallel with the z-axis and the zero point was in the middle of the double lipid layer. The information for the necessary rotation was taken from the PDBTM database []. The proteins were cut into 1Å wide slices parallel to the membrane plane, and the number of polymorphisms and disease associated mutations as well as the number of all residues were […]

library_books

Statistical prediction of protein structural, localization and functional properties by the analysis of its fragment mass distributions after proteolytic cleavage

2016
Sci Rep
PMCID: 4770285
PMID: 26924271
DOI: 10.1038/srep22286

[…] ta from the general proteomic databases UniProtKB/Swiss-Prot and RSCB PDB, from the databases of intrinsically disordered proteins DisProt and Ideal as well as from the transmembrane protein database PDBTM and the bacterial virulence factors database VFPB. We follow a unified procedure to prepare the datasets for the analysis including removal of items containing illegal symbols and elimination of […]

library_books

Prediction of Protein Protein Interaction Sites Based on Naive Bayes Classifier

2015
PMCID: 4677168
PMID: 26697220
DOI: 10.1155/2015/978193

[…] a protein complexes is defined as missing residue number in a protein sequence/length of the sequence. Eliminate any protein complexes with a missing ratio of ≥30%.Transmembrane proteins recorded in PDBTM were removed.PDBsum was used to retain protein complexes with interface area between 500 Å2 and 2500 Å2.Some of the remaining dimeric protein complexes, determined by above filters, that may be […]

Citations

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PDBTM institution(s)
Lendület Membrane Protein Bioinformatics Research Group and Protein Structure Research Group, Institute of Enzymology, Budapest, Hungary
PDBTM funding source(s)
This work was supported by grants n°BIO0005/2001, OTKAT34131, D42207 and F043609.

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