Tag: protein folds and structural domains


Found 58 sources
Source Match ReputationScore*

Pfam


The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pf ...
100%

Conserved Domain Database


The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and p ...
81%

CATH Protein Structure Classification


The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class ( ...
77%

Simple Modular Architecture Research Tool


SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. It allows the identification and annotation of geneti ...
77%

Saccharomyces Genome Database


The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it.
73%

Structural Classification Of Proteins


The SCOP database is a curated both manually and with the use of automated tools. This freely available resource aims to provide a comprehensive description of the structural and evolutionary relationships between all proteins whose structure is know ...
72%

SUPERFAMILY


SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
62%

ProDom


ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.
58%

CAPS-DB : a structural classification of helix-capping motifs


CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical c ...
54%

Open Provenance Model


The Open Provenance Model (OPM) is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. ( ...
52%

PASS2


PASS2 contains alignments of structural motifs of protein superfamilies. PASS2 is an automatic version of the original superfamily alignment database, CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies). PASS2 con ...
52%

Protein Circular Dichroism Data Bank


The Protein Circular Dichroism Data Bank (PCDDB) is an open-access online repository for protein circular dichroism spectral- and meta-data. Users may freely extract and deposit validated data and the validation process is conveniently integrated int ...
51%

MiST 3.0: Microbial Signal Transduction database


Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated Microbial Signal Transduct ...
51%

Termini-Oriented Protein Function INferred Database


TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alte ...
51%

3D interacting domains


The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details neces ...
51%

Gene3D


Gene3D takes CATH domain families (from PDB structures) and assigns them to the millions protein sequences (using Hidden Markov models generated from HMMER) with no PDB structures.
49%

RBPDB


RNA-binding proteins and their specificities
47%

DNASU Plasmid Repository


DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 197,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure I ...
46%

Mammalian Protein Localization Database


LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.
46%

Intrinsically Disordered proteins with Extensive Annotations and Literature


IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature) is a collection of experimentally-verified intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. IDEAL ...
45%

FunTree: A Resource For Exploring The Functional Evolution Of Structurally Defined Enzyme Superfamilies


A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function.
45%

UniProtKB Swiss-Prot


Manually annotated component of UniProtKB (produced by the UniProt consortium). It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.
44%

Protein Model Portal


Developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a c ...
43%

DOMINE


Known and predicted protein domain interactions observed in PDB entries,
42%

SitEx database of eukaryotic protein functional sites


SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in ...
41%

Effective


Predicted secreted bacterial proteins
41%

ProtCID


Protein Common Interface Database
41%

Negatome


A database of non-interacting proteins
41%

PDBselect


PDBselect (http://bioinfo.tg.fh-giessen.de/pdbselect/) is a list of representative protein chains with low mutal sequence identity selected from the protein data bank (PDB) to enable unbiased statistics. The list increased from 155 chains in 1992 to ...
41%

Indel Flanking Region Database


Indel Flanking Region Database is an online resource for indels (insertion/deletions) and the flanking regions of proteins in SCOP superfamilies. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid indels, substitut ...
40%

Brix


Protein building blocks for structural analysis, modeling and design
39%

ThYme


Thioester-active enzymes
39%

ComSin


Protein structures in bound and unbound states
39%

DIMA


Domain interaction map: experimental and predicted protein domain interactions
39%

Protein Geometry Database


Protein conformation and bond angles and lengths
38%

FunShift


Functional divergence between the subfamilies of a protein domain family
38%

ADPriboDB


ADP-ribosylated proteins and sites
38%

PhaSePro


Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multiv ...
38%

PolyQ


Polyglutamine Repeats in Proteins
38%

PCDB


Protein Conformational Diversity database
38%

MeMotif


Linear motifs in alpha-helical transmembrane proteins
37%

BSDB


Biomolecule Stretching Database
37%

TMPad


The TransMembrane Protein Helix-Packing Database (TMPad) is an integrated repository of experimentally determined structural folds derived from helix-helix interactions in alpha-helical membrane proteins. TMPad includes geometric descriptors of helix ...
37%

DOMMINO


Database of MacroMolecular INteractions
37%

Start2Fold


Hydrogen/deuterium exchange data on protein folding and stability
37%

SAHG


Structural Atlas of Human Genome
37%

MutationAligner


Somatic mutation hotspots in protein domains in cancer
36%

SPRITE


SPRITE is a protein structural motif database searching program. Users can upload a PDB file of a query protein structure, and SPRITE compares the input coordinates to a database of 3D side chain arrangements of sites and motifs using a graph theoret ...
36%

PTGL


Protein Topology Graph library: Secondary structure-based protein topologies
35%

CDDB


Database for comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a coarse-grained computational approach that is applied to most structures present in the electron ...
34%

BacFITBase


A database to assess the relevance of bacterial genes during host infection. Bacterial Fitness In infecTion dataBase. Host species Any host species Cow (Bos taurus) Chicken (Gallus gallus) Mouse (Mus musculus) Rabbit (Oryctolagus cuniculus) Pig (Su ...
33%

MANET


Hierarchy and modularity in evolving metabolic networks. Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online re ...
32%

PerMemDB


A database for eukaryotic peripheral membrane proteins. The majority of all proteins in cells interact with membranes either permanently or temporarily. Peripheral membrane proteins form transient complexes with membrane proteins and or lipids, via ...
32%

Lipase Engineering Database


The Lipase Engineering Database (http://www.led.uni-stuttgart.de) integrates information on sequence, structure, and function of lipases, esterases, and related proteins. Sequence data on 806 protein entries are assigned to 38 homologous families, wh ...
32%

RRMdb


Evolutionary-oriented database of RNA recognition motif sequences.
30%

ImmunoDB


A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.
30%

AniProtDB


The Animal Proteome Database (AniProtDB) is a comprehensive collection of proteomes from 100 species spanning 21 animal phyla. In addition to providing open access to this collection of high-quality metazoan proteomes, information on predicted protei ...
30%

DistAA


Database of amino acid distances in proteins and web application for statistical review of distances. Three-dimensional structure of a protein chain is determined by its amino acid interactions. One approach to the analysis of amino acid interaction ...
30%

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