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Protein structures database | Protein structure data analysis

ModBase
Dataset

ModBase

A queryable database of annotated protein structure models. ModBase models are…

A queryable database of annotated protein structure models. ModBase models are derived by ModPipe, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database also…

EBI
Dataset

EBI EMBL-EBI - The European Bioinformatics Institute

Supplies an access to several biological data resources. EBI is a database that…

Supplies an access to several biological data resources. EBI is a database that covers the entire range of biological sciences: raw DNA sequences to curated proteins, chemicals, structures, systems,…

SWISS-MODEL…
Dataset

SWISS-MODEL Repository

Provides access to an up-to-date collection of annotated 3D protein models…

Provides access to an up-to-date collection of annotated 3D protein models generated by automated homology modelling for relevant model organisms and experimental structure information for all…

PDBsum
Dataset

PDBsum

Provides overviews and pictorial analyses of the experimentally determined…

Provides overviews and pictorial analyses of the experimentally determined models of macromolecular structures in the Protein Data Bank (PDB). PDBsum depicts the molecules in each entry and shows…

PDB_REDO
Dataset

PDB_REDO

Optimizes crystallographic structure models. PDB_REDO contains algorithm which…

Optimizes crystallographic structure models. PDB_REDO contains algorithm which allows the setting up of an automated decision making system. This system serves for refinement, rebuilding and…

CSA
Dataset

CSA Catalytic Site Atlas

A database documenting enzyme active sites and catalytic residues in enzymes of…

A database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be…

MolMovDB
Dataset

MolMovDB Database of Macromolecular Movements

Allows users to make structural analysis. MolMovDB consists of a set of coupled…

Allows users to make structural analysis. MolMovDB consists of a set of coupled hypertext pages with graphic images and a simple query box. It offers a lot of tools to systematize all instances of…

CyBase
Dataset

CyBase

Provides information about cyclic proteins. Cybase aims to compile a…

Provides information about cyclic proteins. Cybase aims to compile a standardized library gathering proteic sequences, nucleic sequences, 3D structures and assay results. Moreover, the database…

SoyKB
Dataset

SoyKB Soybean Knowledge Base

A comprehensive web resource developed for bridging soybean translational…

A comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs,…

HUGE
Dataset

HUGE Human Unidentified Gene-Encoded

Stores results from sequence analysis of human novel large complementary DNA…

Stores results from sequence analysis of human novel large complementary DNA (cDNAs) obtained in the context of the Kazusa cDNA sequencing Project. HUGE is a database than contains more than 2000…

OCA
Dataset

OCA

A browser-database for protein structure/function. OCA database integrates…

A browser-database for protein structure/function. OCA database integrates information from KEGG, OMIM,PDBselect, Pfam, PubMed, SCOP, SwissProt, and others. It provides rich content annotation on…

Phospho3D
Dataset

Phospho3D

Supplies a repository composed of 3D structures of phosphorylation sites…

Supplies a repository composed of 3D structures of phosphorylation sites (P-sites) stemmed from the Phospho.ELM database. Phospho3D enhances data from the previous database at the residue level with…

CCDB
Dataset

CCDB CyberCell DataBase

A comprehensive collection of detailed enzymatic, biological, chemical,…

A comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655).

PMDB
Dataset

PMDB Protein Model Database

Allows deposit and retrieval of built 3D models of proteins with their…

Allows deposit and retrieval of built 3D models of proteins with their supporting information. PMDB is a relational database of protein models submitted by users and obtained with different structure…

PMD
Dataset

PMD Protein Mutant Database

Provides a compilation of protein mutant data, providing information on…

Provides a compilation of protein mutant data, providing information on functional and/or structural influences brought about by amino acid mutations at specific positions of a protein. PMD is an…

PSI SGKB
Dataset

PSI SGKB Protein Structure Initiative Structural Genomics Knowledgebase

Provides results of the protein structure initiative (PSI). PSI SGKB is a…

Provides results of the protein structure initiative (PSI). PSI SGKB is a knowledge base that supplies access to the annotated protein structures, associated functional predictions, experimental…

EchoBASE
Dataset

EchoBASE

Contains some information from post-genomic experiments that use the model…

Contains some information from post-genomic experiments that use the model bacterium Escherichia coli K12. EchoBASE allows consultation of protein–protein interaction (PPI) data, structural data…

ProtCid
Dataset

ProtCid Protein Common interfaces database

A database that contains clusters of similar homodimeric and heterodimeric…

A database that contains clusters of similar homodimeric and heterodimeric interfaces observed in multiple crystal forms (CFs). Such interfaces, especially of homologous but non-identical proteins,…

PDBe
Dataset

PDBe Protein Data Bank in Europe

Accepts and annotates depositions of macromolecular structure data in the PDB…

Accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website…

SURFACE
Dataset

SURFACE SUrface Residues and Functions Annotated Compared and Evaluated

Stores and spreads the results of a large-scale local surface comparison…

Stores and spreads the results of a large-scale local surface comparison experiment. SURFACE is a relational database that allows scientific community to retrieve non-obvious functional similarities…

MegaMotifbase
Dataset

MegaMotifbase

Gathers structural segments or motifs for protein structures. MegaMotifbase…

Gathers structural segments or motifs for protein structures. MegaMotifbase provides a compilation of structural motifs identified through a completely automated method for large number of families…

3D Complex
Dataset

3D Complex

A hierarchical classification of protein complexes that describes similarities…

A hierarchical classification of protein complexes that describes similarities in structure, sequence, as well as topology of contacts of the constituent proteins.

DBETH
Dataset

DBETH Database for Bacterial ExoToxins

The main objective of this database is to provide a comprehensive knowledgebase…

The main objective of this database is to provide a comprehensive knowledgebase for human pathogenic bacterial toxins where various important sequence, structure and physico-chemical property based…

FSN
Dataset

FSN Flexible Structural Neighborhood

Compiles structural neighbors of proteins deposited in the Protein Data Bank…

Compiles structural neighbors of proteins deposited in the Protein Data Bank (PDB). FSN allows to search by a PDB code as a query and provides a list of structurally similar proteins sorted by…

PPT-DB
Dataset

PPT-DB

A database of protein property databases.

A database of protein property databases.

FLAGdb++
Dataset

FLAGdb++

Helps biologists to find the flanking insertion sites (FSTs) that interrupt the…

Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant…

ProtChemSI
Dataset

ProtChemSI protein-chemical structural interactions

Gathers information and data about protein-chemical topic. ProtChemSI is a…

Gathers information and data about protein-chemical topic. ProtChemSI is a resource that contains known structures of protein–chemical complexes and several other predicted complexes. The web…

PDB-facilities
Dataset

PDB-facilities

A series of databanks that hold information that is computationally derived…

A series of databanks that hold information that is computationally derived from Protein Data Bank (PDB) entries and that might augment macromolecular structure studies. These derived databanks run…

CDDB
Dataset

CDDB Conformational Dynamics Databank

Gathers conformational dynamics information for structures deposited in the…

Gathers conformational dynamics information for structures deposited in the electron microscopy data bank (EMDB). CDDB includes data about conformational flexibility, dynamical coupling between…

AH-DB
Dataset

AH-DB Apo and Holo structures DataBase

Provides sophisticated interfaces for searching apo–holo structure pairs.…

Provides sophisticated interfaces for searching apo–holo structure pairs. AH-DB allows users to explore conformational transitions from apo structures to the corresponding holo structures. It…

Cyclo-lib
Dataset

Cyclo-lib

A database with structural and dynamic analysis obtained from computational MD…

A database with structural and dynamic analysis obtained from computational MD simulation trajectories of native and modified cyclodextrins (CDs) in explicit water molecules. Cyclo-lib currently…

SAHG
Dataset

SAHG Structure Atlas of Human Genome

Provides 3D models and other annotations for protein functions. SAHG is a…

Provides 3D models and other annotations for protein functions. SAHG is a database that permits the access of human proteins examined by local alignment methods (BLAST, PSI-BLAST and Smith–Waterman…

PTGL
Dataset

PTGL Protein Topology Graph Library

Allows user to retrieve and search specific protein topologies. PTGL provides…

Allows user to retrieve and search specific protein topologies. PTGL provides searching facilities using sequence similarity in proteins. The web platform of this database has four query browsers:…

SFLD
Dataset

SFLD The Structure–Function Linkage Database

A manually curated classification resource describing structure–function…

A manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. SFLD focuses on the identification of specific sequence and…

PDBj
Dataset

PDBj Protein Data Bank Japan

Maintains a centralized PDB archive of macromolecular structures and provides…

Maintains a centralized PDB archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU. The Protein Data Bank Japan is a…

CMGSDB
Dataset

CMGSDB Database for Computational Modeling of Gene Silencing

An integration of heterogeneous data sources about Caenorhabditis elegans with…

An integration of heterogeneous data sources about Caenorhabditis elegans with capabilities for compositional data mining (CDM) across diverse domains.

KIXBASE
Dataset

KIXBASE

Detects the presence of kinase-inducible domain interacting (KIX) domains.…

Detects the presence of kinase-inducible domain interacting (KIX) domains. KIXBASE is based on computational meta-analysis of available data and Hidden Markov Model (HMM) domain identification…

Cysteinome
Dataset

Cysteinome

Compiles information about proteins with targetable cysteine and their covalent…

Compiles information about proteins with targetable cysteine and their covalent modulators among multiple species. Cysteinome is a manually curated database which aims to describe functions and…

AmyPro
Dataset

AmyPro

Offers a sequence screening service allowing users to screen sequences of…

Offers a sequence screening service allowing users to screen sequences of interest for matching fragments with validated amyloidogenic regions. AmyPro provides comprehensive information on the entry…

ChannelsDB
Dataset

ChannelsDB

Provides information about the channels (pores and tunnels) found in entries…

Provides information about the channels (pores and tunnels) found in entries from the Protein Data Bank (PDB). ChannelsDB is a resource that contains information about the presence and positions of…

dspp
Dataset

dspp database of structural propensities of proteins

Gives access to structural propensities of proteins. dspp is derived from a…

Gives access to structural propensities of proteins. dspp is derived from a subset of 7094 nuclear magnetic resonance (NMR) assignments of unrelated proteins in solution and solid state near…

MUFOLD-DB
Dataset

MUFOLD-DB

Allows users to collect and process the weekly Protein Data Bank (PDB) files.…

Allows users to collect and process the weekly Protein Data Bank (PDB) files. MUFOLD-DB provides a web interface for users to browse, search and download several types of data. This database includes…

ccPDB
Dataset

ccPDB Compilation and Creation of datasets from PDB

Hosts data sets compiled from the literature and Protein Data Bank (PDB). ccPDB…

Hosts data sets compiled from the literature and Protein Data Bank (PDB). ccPDB collects and compiles data sets from the literature used for developing bioinformatics methods to annotate the…

BriX
Dataset

BriX

A vast database of protein fragments, clustered on their backbone similarity.

A vast database of protein fragments, clustered on their backbone similarity.

PACSY
Dataset

PACSY Protein structure And Chemical Shift NMR spectroscopy

A relational database management system that integrates information from the…

A relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database.…

CSANDS
Dataset

CSANDS Coding Sequence and Structure

Simplifies a comprehensive analysis of codon usage. CSANDS provides an…

Simplifies a comprehensive analysis of codon usage. CSANDS provides an accurate, curated mapping between over 4400 protein structures and the mRNA that encodes them. It makes a comprehensive analysis…

PFF
Dataset

PFF Protein Folding Fragments Consortium

Contains protein structural fragments and their application for protein…

Contains protein structural fragments and their application for protein engineering and misfolding related diseases.

OLIGAMI
Dataset

OLIGAMI OLIGomer Architecture and Molecular Interface

Gathers verified coordinates for the biological molecules for all Protein Data…

Gathers verified coordinates for the biological molecules for all Protein Data Bank (PDB) entries. OLIGAMI is a database allowing to (i) visualize 3D structures of biological molecules, (ii) browse…

PrFEcT-Predict
Dataset

PrFEcT-Predict

Provides a compilation of resources about several proteomes. PrFEcT-Predict…

Provides a compilation of resources about several proteomes. PrFEcT-Predict contains precomputed 3D structure models, secondary structure predictions, disordered regions, and predicted functions.

PSILO
Dataset

PSILO

Gathered information about macromolecular and protein-ligand structural…

Gathered information about macromolecular and protein-ligand structural information. PSILO intends to provide a customised storage which allows searches and dynamic vizualisation among macromolecular…

2D-PAGE
Dataset

2D-PAGE

Stores and manages proteomics data. 2D-PAGE may be used to publish…

Stores and manages proteomics data. 2D-PAGE may be used to publish two-dimensional electrophoretic proteomics data, and also may be accessed by external users who want to compare their own data with…

PALI
Dataset

PALI Phylogeny and ALIgnment of homologous protein structures

Comprises a compendium of homologous protein structures with pairwise, multiple…

Comprises a compendium of homologous protein structures with pairwise, multiple structural alignments and phylogenetic dendrograms. PALI provides a user-friendly web interface for associating a query…

GTOP
Dataset

GTOP Genomes TO Protein Structures and Functions database

Compiles several annotations of 3D structures, protein families, functions…

Compiles several annotations of 3D structures, protein families, functions about proteins. GTOP intends to supply annotations of all the amino acid sequences of proteins derived from all the…

PGD
Dataset

PGD Protein Geometry Database

Allows exploration of peptide geometry, peptide conformation, and the ties…

Allows exploration of peptide geometry, peptide conformation, and the ties between them. PGD contains derived data for a complete, representative data set of protein structures that are relevant to…

MulPSSM
Dataset

MulPSSM Multiple position-specific scoring matrices

Consists of position-specific scoring matrices (PSSMs) of protein domain…

Consists of position-specific scoring matrices (PSSMs) of protein domain sequence and structural families. MulPSSM is a web-based database which allows users to select datasets of PSSMs corresponding…

ProtrWeb
Web
Desktop

ProtrWeb

Calculates various commonly used structural and physicochemical descriptors and…

Calculates various commonly used structural and physicochemical descriptors and proteochemometrics modeling descriptors for amino acid sequences. Users can select appropriate descriptors calculated…

ExDom
Dataset

ExDom

Compiles the exon–intron structure of protein domains from seven eukaryotic…

Compiles the exon–intron structure of protein domains from seven eukaryotic genomes. ExDom provides reliable one-tone mapping of domain data from the Pfam database to exon–intron structure…

PIDD
Dataset

PIDD Protein Inter-Atomic Distance Distribution Database

Gathers information on how the inter-atomic distances are formed as revealed in…

Gathers information on how the inter-atomic distances are formed as revealed in their distributions in known proteins. PIDD allows calculation and storage of the distributions of the distances in…

PFD
Dataset

PFD Protein Folding Database

Provides data about protein folding. PFD provides annotated information,…

Provides data about protein folding. PFD provides annotated information, enriched with experimental, structural and functional details. It is searchable using many parameters, as well as retrieval…

SPrCY
Dataset

SPrCY Structure Prediction Comparison for Yeast

Compares predictions of several fold-recognition techniques to the…

Compares predictions of several fold-recognition techniques to the Saccharomyces cerevisiae genome. SPrCY is a database which allows users to search, browse and analyze the generated predictions. It…

DMAPS
Dataset

DMAPS Database of Multiple Alignments for Protein Structures

Provides access to multiple structure alignments for all protein families in…

Provides access to multiple structure alignments for all protein families in the Protein Data Bank (PDB). DMAPS is a database of multiple alignments for protein structures containing data classified…

SKPDB
Dataset

SKPDB ShiKimate Pathway DataBase

Provides data about protein structure predicted by comparative modeling or…

Provides data about protein structure predicted by comparative modeling or solved by X-ray crystallography, applied to the study of shikimate pathway enzymes of microorganisms and plants. SKPDB…

DetoxiProt
Dataset

DetoxiProt

Facilitates annotation and acquisition of information about the detoxification…

Facilitates annotation and acquisition of information about the detoxification proteins. DetoxiProt is a database for detoxification protein researchers in the fields of physiology, pharmacology,…

KiBank
Dataset

KiBank

A database of inhibition constant (Ki) values with 3D structures of target…

A database of inhibition constant (Ki) values with 3D structures of target proteins and chemicals. Ki values were accumulated from peer-reviewed literature searched via PubMed. The 3D structure files…

PDBWiki
Dataset

PDBWiki

A scientific wiki for the community annotation of protein structures. The wiki…

A scientific wiki for the community annotation of protein structures. The wiki consists of one structured page for each entry in the Protein Data Bank (PDB) and allows the user to attach categorized…

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