Servers and databases

# Name Url Year Visitors Completed tasks/downloads
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 1361807 15177533
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 1203609 4618539
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 30183 n.a.
SRide identifies residues expected to play key roles in the stabilization of proteins.
7 TMDET http://tmdet.enzim.hu 2005 525387 110185
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 1133541 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 2854843 2972030
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 41261 26649
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 390383 32260
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 2516 1012
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 23725 2869
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 223785 1754
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 3815 21024
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 10087 39467
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 39324 361109
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 3087 454898
The leishMANIAdb contains experimental, computational and annotated information about proteins from Leishmania species.
23 UniTmp/PDBTM https://pdbtm.unitmp.org 2023 263822 942809
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 60401 44523
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 381030 256449
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 75816
TOPDOM is a collection of domains and sequence motifs located conservatively in one side of transmembrane proteins.
27 BETA https://beta.pbrg.hu 2024 11803 21
BETA provides datasets of structures and sequences that were not used during AlphaFold2 training.
Sum 11204200 26561493