Analyses of PDBID
In past number of web servers have been developed to extract useful information from tertiary structure. These servers allows users to perform anlysis on their structure (PDB ID). These servers are scattered on Internet, it very difficult for users to use their potentials. We collected more than 40 servers from literature and developed a meta server, where user can submit PDB ID once and can got information about PDB ID from any of these server. This page allows analysis from single plateform.
PDB ID: 6cny submitted, for more information on this PDB ID, click any of the following server/databases
| Name | Description | Category |
| PDB | Protein Data Bank (PDB) is a archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. | Structure Summary |
| ProteoPedia | Proteopedia is a wiki, 3D encyclopedia of proteins and other molecules. The site contains a page for every entry in the PDB. | 3D interactive encyclopedia of proteins |
| EBI's EB-eye | The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the European Bioinformatics Institute | protein structure/function |
| PDBsum | PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them. | Structure Summary |
| EDS | The Uppsala Electron Density Server (EDS) provides the scientific community with a service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. | evaluating the electron density of crystal structures |
| PDBe | Protein Data Bank in Europe (PDBe) is the the collection, management and distribution of data about macromolecular structures, derived from the Protein Data Bank (PDB). | Structure Summary |
| PDB REDO | PDB REDO is the method for automated re-refinement of structure models in the PDB. | macromolecular X-ray diffraction structure models |
| Procheck | PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. | stereochemical analysis |
| CASTp | Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. | Structure Features |
| SCOP | Structural Classification of Proteins (SCOP) is a structural classification of proteins database, provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. | Structure Classification |
| CATH | Protein Structure Classification (CATH) is a semi-automatic, hierarchical classification of protein domains. The four main levels of this classification are protein class (C), architecture (A), topology (T) and homologous superfamily (H). | Structure Classification |
| VAST | Vector Alignment Search Tool (VAST) is NCBI's structure-structure similarity search service. It compares 3D coordinates of a newly determined protein structure. | Structure Classification and Comparison |
| DSSP | Dictionary of protein secondary structure (DSSP) is a program o standardize secondary structure assignment. | Secondary Structure |
| fireDB | fireDB is a database of PDB structures and their associated ligands. fireDB also contains the largest set of reliably annotated functionally important residues. | Functional annotation |
| PDB File | Download PDB file. | PDB file |
| Sequence | Download fasta sequence. | fasta sequence |
| Ramachandran plot of 6cny | The Ramachandran plot shows the phi-psi torsion angles for all residues in the structure (except those at the chain termini). | Ramachandran plot |
| MMDB | Molecular Modeling Database (MMDB) is a database of experimentally resolved structures of proteins, RNA, and DNA, derived from the Protein Data Bank (PDB), with value-added features such as explicit chemical graphs, links to literature, similar sequences, related 3D structures, information about chemicals bound to the structures, and more. | Structure Summary |
| PQS | Protein Quaternary Structure server (PQS) is a server allows for searching of the list of likely quaternary structures generated at the EBI. The system is a SQL front end to a database on characteristics of the quaternary structure files. | Protein Quaternary Structure |
| ProSAT | Protein Structure Annotation Tool (ProSAT) is a tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein | 3D structure |
| AffinDB | AffinDB is a affinity database For Protein-Ligand Complexes. | Binding Affinity |
| PDBj | PDBj (Protein Data Bank Japan) maintains a centralized archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU. | Structure/Function summary |
| PDBCartoon | PDB Cartoon produces the image of the amino acid sequence along with the secondary structure elements, rendered as cartoons. | Visualization |