Databases developed and maintained by Hungarian bioinformaticians

ARN

ARN, Autophagy Regulatory Network database

Description:
The ARN database contains proteins involved in the mechanisms of autophagy, their regulators, and their TF and miRNA regulators as well as connections between all these components and signaling pathways. The core of ARN come from manually curated dataset, but it contains also integrated and predicted data from numerous sources, which are available in different layers (autophagy proteins, direct regulators, post-transcriptional, post-translational and miRNA regulators). Data in ARN can be downloaded and filtered according to two aspects (resource, type of interaction) in different file formats(csv, biopax, psimi tab, psimi xml, sbml, cys).
Developer(s):
Tamás Korcsmáros
Institute(s):
ELTE Faculty of Science Department of Genetics
DT40 Genome

DT40 Genome: The genome sequence of the chicken DT40 bursal lymphoma cell line

Description:
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.
Developer(s):
Gábor Tusnády, János Molnár and Dávid Szüts
Institute(s):
Institute of Enzymology, RCNS, HAS
FixPred

FixPred: a resource for correction of erroneous protein sequences

Description:
The FixPred computational pipeline automatically corrects sequences identified by MisPred as erroneous. The associated FixPred database contains corrected UniProtKB/Swiss-Prot and NCBI/RefSeq sequences from Homo sapiens, Mus musculus, Rattus norvegicus, Monodelphis domestica, Gallus gallus, Xenopus tropicalis, Danio rerio, Fugu rubripes, Ciona intestinalis, Branchostoma floridae, Drosophila melanogaster and Caenorhabditis elegans.
Developer(s):
Alinda Nagy and László Patthy
Institute(s):
Institute of Enzymology, RCNS, HAS
HAEdb

HAEdb: C1 inhibitor gene mutation database

Description:
HAEdb is a locus specific mutational database for the gene (SERPING1, C1IN, C1NH) encoding Plasma protease C1 inhibitor protein. The database contains disease-causing mutations (discovered in patients with the autosomal dominant Hereditary angioneurotic oedema) and common polymorphisms as well. The database is community based, research groups are uploading mutations they discover.
Developer(s):
Lajos Kalmár
Institute(s):
Institute of Enzymology, RCNS, HAS
HTP

HTP: The Human Transmembrane Proteome

Description:
The Human Transmembrane Proteome database and web service are 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.
Developer(s):
László Dobson, István Reményi and Gábor Tusnády
Institute(s):
Institute of Enzymology, RCNS, HAS
MisPred

MisPred: a resource for identification of erroneous protein sequences in public databases.

Description:
The MisPred database and computational pipeline provide efficient means for the identification of erroneous sequences in public databases. The MisPred database contains a collection of abnormal, incomplete and mispredicted protein sequences identified as erroneous by MisPred quality control tools in the UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, NCBI/RefSeq and EnsEMBL databases.
Developer(s):
Alinda Nagy and László Patthy
Institute(s):
Institute of Enzymology, RCNS, HAS
PDBTM

PDBTM: Protein Data Bank of Transmembrane Proteins

Description:
PDBTM is the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB) that contains the estimated orientation of the proteins relative to the membrane.
Developer(s):
Tusnády Gábor és Dosztányi Zsuzsanna
Institute(s):
ProtDict

Protein Dictionary

Description:
ProtDict is a UniProt based Protein dictionary, capable of finding UniProt entries based on AC numbers, SwissProt IDs, EC numbers, multiple types of names, and dozens of different types of database cross references.
Developer(s):
Dániel Bánky, Rafael Ördög and Gábor Iván
Institute(s):
Uratim Kft. & ELTE PIT Bioinformatics Group
SignaLink

SignaLink, a signaling pathway resource with multi-layered regulatory networks

Description:
SignaLink contains manually curated molecular information about seven major pathways (RTK, TGF-β, WNT/Wingless, Hedgehog, JAK/STAT, Notch and NHR) in three eukaryotic species (Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster). The signaling pathways are available in one network therefor the interactions between them can be easily examined. The multi-layered (onion-like) database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. Data in SignaLink can be downloaded and filtered according to many aspects (species, pathway, resource, type of interaction) in different file formats (csv, biopax, psimi tab, psimi xml, sbml, cys).
Developer(s):
Tamás Korcsmáros
Institute(s):
ELTE Faculty of Science Department of Genetics
TOPDB

TOPDB: Topology Data Bank of Transmembrane Proteins

Description:
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.
Developer(s):
Gábor Tusnády, László Dobson and Tamás Langó
Institute(s):
Institute of Enzymology, RCNS, HAS
TOPDOM

TOPDOM: Conservatively Located Domains and Motifs in Proteins

Description:
TOPDOM is a collection of domains and sequence motifs located conservatively in one side of transmembrane proteins.
Developer(s):
Gábor Tusnády, Julia Varga and László Dobson
Institute(s):
Institute of Enzymology, RCNS, HAS
TSTMP

TSTMP: Target Selection for human TransMembrane Proteins

Description:
TSTMP is a database designed to help the target selection of human transmembrane proteins for structural genomics projects. The database contains human transmembrane proteins with two or more transmembrane segments considering the existence of an exact 3D structure, or the possibility of an existing model structure for the protein, or the necessity of a new structure for modeling the protein. The database was built by sorting out human proteins with known structure and searching for suitable model structures for the remaining proteins. Proteins without 3D structure or proper model structure were then searched for homologues among the human transmembrane proteins to select targets whose successful structure determination would lead to the best structural coverage of the human transmembrane proteome.
Developer(s):
Gábor Tusnády, István Reményi, Julia Varga és László Dobson
Institute(s):
Institute of Enzymology, RCNS, HAS