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Analyze of PDB ID

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.

Please Enter PDB ID:

PDB ID: 2pdt 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
OCA OCA integrates data from several sources, it allows the user to rapidly search through the contents of the entire PDB Archive for entries obeying certain constraints. protein structure/function
TOPSAN The Open Protein Structure Annotation Network (TOPSCAN) is a novel way to collect, share and distribute information about protein 3D structures and give knowledge about functions and roles of these proteins in their respective organisms. protein 3D structures
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
PDBwiki PDBWiki is a user contributed database of protein structure annotations, listing all the protein structures currently available in the PDB. Structure Summary
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
PDBREPORT The PDBREPORT is a database of observed anomalies in PDB files. PDBREPORT entries can be seen as error reports for macromolecular structures deposited in the PDB. describing structural problems in PDB entries
LPC Ligand Protein Contact (LPC) is a software which gives detailed analysis of interatomic contacts,calculate the solvent-accessible surface of every atom,determine the contacting residues and type of interaction. Structure Features
CSU Contacts of Structural Units (CSU) is a tools which describe the contacts of structural units such as helices, sheets, strands and residues. Structure Features
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
GNM Guassian Network Model (GNM) is a web-based system that describing high-throughput analysis of the collective dynamics of proteins. Visualizing
Chem-BLAST Chemical Block Layered Alignment of Substructure Technique (Chem-BLAST) is a chemical taxonomy-based search engine which search on the fragments of an inhibitor to look for its chemical structural neighbors. Ligand Features
PubChem PubChem is a database of chemical molecules which is maintained by the NCBI. PubChem provides information on the biological activities of small molecules. Ligand 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
FATCAT Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) is a flexible protein structure comparison algorithm, which automatically identifies hinges and internal rearrangements in two protein structures. Structure Alignment and Comparison
DSSP Dictionary of protein secondary structure (DSSP) is a program o standardize secondary structure assignment. Secondary Structure
CSA The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. enzyme active sites
PDB chain identifiers PDB chain identifiers is identify the chain is specified in the PDB file. PDB chain identifier
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 2pdt The Ramachandran plot shows the phi-psi torsion angles for all residues in the structure (except those at the chain termini). Ramachandran plot
SCOPOI SCOPPI (Structural Classification of Protein-Protein Interfaces) is a database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. Protein-Protein Interfaces
DIP Datbase of Interacting Proteins (DIP) is a database of experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. protein-protein interactions
SRS link at EBI SRS is a proven and scalable data integration platform that is used at over 300 commercial and academic sites delivering genomic data to thousands of users. data integration platform
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
FSSP Families of structurally similar proteins (FSSP) is a database of structural alignments of proteins in the Protein Data Bank (PDB). structural alignments
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
PISAProtein Interfaces, Surfaces and Assemblies (PISA) is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies Protein Interfaces, Surfaces
JenaLib The Jena Library of Biological Macromolecules (JenaLib) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. Visualization and analysis
PDBCartoon PDB Cartoon produces the image of the amino acid sequence along with the secondary structure elements, rendered as cartoons. Visualization
XDom A Graphical Tool for Protein Domain and Exon Position Visualization (XDom). Domain Information
WebMol Complete Structure Visualization Visualization
Jena3D Complete Structure Visualization Visualization