| 1 |
SCIDE
|
This server was shut down in 2015.
|
1997 |
n.a.
|
n.a.
|
|
|
SCIDE can identify the stabilization center residues in known protein structures.
|
| 2 |
HMMTOP
|
http://www.enzim.hu/hmmtop
|
1999 |
1359337
|
15176467
|
|
|
HMMTOP predicts topology of transmembrane proteins (i.e. number and positions of
transmembrane helices in the amino acid sequences, and the orientation of sequence parts between
helices relative to the membrane). It utilizes an unsupervised learning algorithm for the prediction
and uses amino acid sequence as input.
|
| 3 |
PSORT-B
|
http://www.psort.org/psortb
|
2003 |
n.a.
|
n.a.
|
|
|
PSORT-B is an updated method of PSORT family for prediction of localization in
Gram-negative bacterial proteins.
|
| 4 |
BiSearch
|
http://bisearch.enzim.hu
|
2004 |
1197936
|
4607972
|
|
|
BiSearch is a primer-design algorithm for DNA sequences. It may be used for both
bisulfite converted as well as for original not modified sequences. Users can search various genomes
with the designed primers to avoid non-specific PCR products.
|
| 5 |
PDBTM
|
This server was shut down in 2023.
|
2004 |
975305
|
72487
|
|
|
PDBTM is the first comprehensive and up-to-date transmembrane protein selection
of the Protein Data Bank (PDB). The database was created by scanning all PDB entries with TMDET
algorithm.
|
| 6 |
SRide
|
http://sride.enzim.hu
|
2005 |
21288
|
n.a.
|
|
|
SRide identifies residues expected to play key roles in the stabilization of proteins.
|
| 7 |
TMDET
|
http://tmdet.enzim.hu
|
2005 |
518471
|
110158
|
|
|
TMDET is an online tool for the detection of the transmembrane regions of membrane
proteins by using their 3D structure only.
|
| 8 |
TOPDB
|
This server was shut down in 2023.
|
2008 |
720126
|
204426
|
|
|
The Topology Data Bank of Transmembrane Proteins (TOPDB) is a complete and comprehensive
collection of transmembrane protein datasets containing experimentally derived topology information.
The database collects the details of various experiments carried out to learn about the topology of
particular transmembrane proteins.
|
| 9 |
TOPDOM
|
This server was shut down in 2023.
|
2008 |
607665
|
1135655
|
|
|
TOPDOM is a collection of domains and sequence motifs located conservatively in one side
of transmembrane proteins.
|
| 10 |
CMWeb
|
http://cmweb.enzim.hu
|
2012 |
1129773
|
8253
|
|
|
Contact Map WebViewer (or shortly, CMWeb) is an online tool for studying basic
properties of residue-residue contact formation and contact clusters.
|
| 11 |
CCTOP
|
https://cctop.ttk.hu
|
2014 |
2835811
|
2891184
|
|
|
CCTOP predicts the topology i.e. localization of membrane spanning regions and
orientation of segments between them for transmembrane proteins. The prediction is a consensus
of 10 different methods enchanced with available structural and experimental information of any
homologous proteins in the TOPDB database.
|
| 12 |
TmFoldWeb
|
This server was shut down in 2021.
|
2015 |
15843
|
1725
|
|
|
TMFoldWeb is a web server for recognizing the fold of the membrane segments of
transmembrane proteins based on statistical potentials and a topology filtering approach.
|
| 13 |
dt40
|
http://dt40.enzim.ttk.mta.hu
|
2015 |
40636
|
25355
|
|
|
In the dt40 homepage a de novo assembly of the DT40 genome can be downloaded or BLAST
searched. Further files with information about the DT40 genome and web links are also provided.
|
| 14 |
TSTMP
|
http://tstmp.enzim.ttk.mta.hu
|
2016 |
390014
|
32238
|
|
|
TSTMP is a database designed to help the target selection of human transmembrane
proteins for structural genomics projects.
|
| 15 |
HTP
|
This server was shut down in 2023.
|
2016 |
315017
|
n.a.
|
|
|
The Human Transmembrane Proteome database and web service are a comprehensive
resources of the α-helical human transmembrane proteins. It contains topology and structure
information about the human α-helical transmembrane proteins classified into reliability levels.
|
| 16 |
MFIB
|
http://mfib.enzim.ttk.mta.hu
|
2017 |
1183
|
418
|
|
|
Mutual Folding Induced by Binding (MFIB) database is a repository for protein complexes that are formed exclusively by intrinsically unstructured proteins (IUPs). As these proteins have no stable tertiary structure in their monomeric form, their folding is induced by the assembly of the complex.
|
| 17 |
TMCrys
|
http://tmcrys.enzim.ttk.mta.hu
|
2018 |
23466
|
2864
|
|
|
TMCrys predicts the probability of successful solubilization, purification and
crystallization of transmembrane proteins as well as the success for all these three steps together.
|
| 18 |
PolarProtDb
|
https://polarprotdb.ttk.hu
|
2020 |
181747
|
1604
|
|
|
PolarProtDb is the most comprehensive database containing experimentally verified
mammalian proteins that display polarized sorting or secretion, focusing at epithelial polarity.
In addition to the source cells or tissues, homology-based inferences and transmembrane topology
(if applicable) are all provided together.
|
| 19 |
MemDis
|
https://memdis.ttk.hu
|
2020 |
2701
|
21021
|
|
|
MEMDIS is a novel prediction method, utilizing convolutional neural network and long short-term memory networks for predicting disordered regions in TMPs. MEMDIS achieved the highest prediction accuracy on TMP specific dataset among other popular IDR prediction methods.
|
| 20 |
PolarProtPred
|
https://polarprotpred.ttk.hu
|
2021 |
8083
|
39316
|
|
|
PolarProtPred may offer help to experimentalists to identify or better characterize
molecular networks regulating the distribution of transporters or surface receptors (including viral
entry receptors like COVID-19) by predicting polar distribution of transmembrane proteins.
|
| 21 |
TmAlphaFold
|
https://tmalphafold.ttk.hu
|
2022 |
36265
|
305654
|
|
|
TmAlphaFold database provides open access to the membrane orientation of all
alpha-helical transmembrane protein's structure predicted by AlphaFold together with the
evaluation of the predicted structures.
|
| 22 |
LeishMANIAdb
|
https://leishmaniadb.ttk.hu
|
2023 |
1727
|
212325
|
|
|
The leishMANIAdb contains experimental, computational and annotated information
about proteins from Leishmania species.
|
| 23 |
UniTmp/PDBTM
|
https://pdbtm.unitmp.org
|
2023 |
247335
|
661985
|
|
|
PDBTM is the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB). The database was created by scanning all PDB entries with TMDET algorithm.
|
| 24 |
UniTmp/HTP
|
https://htp.unitmp.org
|
2023 |
47208
|
31588
|
|
|
The Human Transmembrane Proteome database and web service are a comprehensive resources of the α-helical human transmembrane proteins. It contains topology and structure information about the human α-helical transmembrane proteins classified into reliability levels.
|
| 25 |
UniTmp/TOPDB
|
https://topdb.unitmp.org
|
2023 |
213790
|
249537
|
|
|
The Topology Data Bank of Transmembrane Proteins (TOPDB) is a complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information. The database collects the details of various experiments carried out to learn about the topology of particular transmembrane proteins.
|
| 26 |
UniTmp/TOPDOM
|
https://topdom.unitmp.org
|
2023 |
5835
|
55900
|
|
|
TOPDOM is a collection of domains and sequence motifs located conservatively in one side of transmembrane proteins.
|
| 27 |
BETA
|
https://beta.pbrg.hu
|
2024 |
4085
|
14
|
|
|
BETA provides datasets of structures and sequences that were not used during AlphaFold2 training.
|
|
Sum |
|
|
10900647 |
25848146 |