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Structure Validation and Quality - RCSB PDB
WEBA program that checks the stereochemical quality of a protein structure: Prosa-web: Quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. …
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RCSB PDB: Homepage
WEBComplex boolean queries with values for a wide range of structure attributes. Sequence Similarity Search. Find similar protein and nucleic acid sequences using the mmseqs2 method. Structure Similarity Search. Search protein structures by global shape similarity. Chemical Similarity Search
Structure Prediction - RCSB PDB
WEBAlphaFold Protein Structure Database: AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence: ModelArchive: Repository for theoretical models of macromolecular structures: ModBase: A database of comparative protein structure models: SWISS-MODEL Repository
PDB Validation Suite - RCSB
WEBPDB Validation Suite. The PDB Validation Suite is a set of tools used by the PDB for processing and checking structure data. Note: Binary distribution of Validation Suite contains an additional submodule "procheck", which does additional structure checking.
WEBRCSB Data Format Conversion and Validation Tools. MAXIT Updated! April 21, 2024 – An application for processing and annotating of macromolecular structure data; sf-convert standalone tool – A format conversion standalone tool for structure factor files that supports more than a dozen file formats
PDB-101: Learn: Guide to Understanding PDB Data
WEBR-value and R-free. R-value is the measure of the quality of the atomic model obtained from the crystallographic data. When solving the structure of a protein, the researcher first builds an atomic model and then calculates a simulated diffraction pattern …
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Hierarchical Structure of Proteins - pdb101.rcsb.org
WEBBy understanding the way the protein chain folds into this functional structure, researchers are now beginning to be able to predict the structure of any protein, as with the recent successes in AlphaFold2 and RoseTTAFold, and also …
Structure Classification and Analysis - RCSB PDB
WEBHB plot is a tool for exploring protein structure and function by describing structure as a network of hydrogen bonding interaction. Het-PDB Navi: List of all Het atoms in the PDB, or search by PDB ID or Het code: HOMSTRAD: Homologous Structure Alignment Database: IC50 Calculator: Free IC50 calculator and Computer Aided Drug Design tools and ...
RCSB PDB: Publications
WEBRCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D (2022) Protein Science 31: e4482 doi: 10.1002/pro.4482. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future
Structure Validation and Quality - rcsb.org
WEBAs a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and …
Assessing the Quality of 3D Structures - RCSB PDB
WEBAs a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and …
Pairwise Structure Alignment - RCSB PDB
WEBThis tool presents options for pairwise structure alignment of proteins. In the case of pairwise alignment, structures are always compared in pairs. In contrast to multiple structure alignment (reviewed in Ma and Wang, 2014) that provides a global solution for three or more structures.
Modeling and Simulation Software - RCSB PDB
WEBOpenContact is an open source, PC software tool for quickly mapping the energetically dominant atom-atom interactions between chains or domains of a given protein. A simple GUI is provided to the user to perform the mapping and no knowledge of the underlying programs are required.
View Validation in 3D - RCSB PDB
WEBVisualizing structure quality metrics in three dimensions. On the left is a structure of Endoglucanase A (PDB ID 3WY6) with a generally good fit; on the right a structure of Ribonuclease P protein component 3 (PDB ID 3WYZ), which has areas of more problematic fit.For details regarding RSRZ and RSCC, please consult the Validation …
Using KBase to access PDB Structures and CSMs - RCSB PDB
WEBImport experimental protein structure data into KBase from the RCSB PDB. Upload computed structure models of proteins from AlphaFold or RoseTTAFold into KBase. View experimental structures and computed structure models of proteins in KBase and linking to the broader KBase data resource.
Ligand Structure Quality in PDB Structures - RCSB PDB
WEBThe wwPDB validation report provides validation of individual ligand quality (Feng et al., 2021), including the local electron density goodness-of-fit indicators of real space R factor (RSR) (Jones et al., 1991) and real space correlation coefficient (RSCC) (Brändén and Jones 1990) for X-ray structures as calculated by EDS (Kleywegt et al ...
RCSB PDB - 3D View
WEB3D Structures in the Protein Data Bank ; Computed Structure Models (CSM) Search and Browse ; Basic Search ; Advanced Search ; Browse Annotations ; Visualize and Analyze ; Sequence Viewers ; Pairwise Structure Alignment ; Exploring a 3D Structure
Find Similarly-Shaped Structures with Advanced Search - RCSB …
WEBRCSB.org uses a novel method to quickly detect similarity between protein shapes of any size. Use the Advanced Search>Structure Similarity option to find proteins with similar 3D protein shapes using either a PDB ID or a URL to an external structure data file (mmCIF, BinaryCIF or PDB file format).
Molecular Graphics Software - RCSB PDB
WEBStructures can be downloaded and displayed from the PubChem, PDB, and NCBI structure databases together with the sequences for proteins and nucleic acids. Structures can be drawn as tubes, ball and stick, or space filling modes.
RCSB PDB - Pairwise Structure Alignment Tool
WEBPairwise Structure Alignment. This tool allows the selection of protein 3D structures for alignment. Use an existing PDB or Computed Structure Model entry ID, upload a local file with atomic coordinates, or enter a URL of a file on the web.
NGL - RCSB PDB
WEBAs a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and …
Sequence - RCSB PDB
WEBAs a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and …
Overview of PDB Validation Reports published in Structure
WEBOverview of PDB Validation Reports published in Structure 12/05. An article focused on the structure validation reports produced by wwPDB is now available: Validation of Structures in the Protein Data Bank (2017) Structure 25: 1916-1927 doi: 10.1016/j.str.2017.10.009.
RCSB PDB - 8W01: Crystal structure of DUF1735 domain …
WEBCrystal structure of DUF1735 domain-containing protein (GH18-like) from Bacteroides faecium at 2.7 A resolution (Space group C2) ... Structure Validation. View Full Validation Report. View more in-depth experimental data. Entry History & Funding Information.
RCSB PDB - 8K9K: Full agonist-bound mu-type opioid receptor …
WEB8K9K, 8K9L. PubMed Abstract: G-protein-coupled receptors (GPCRs) play pivotal roles in various physiological processes. These receptors are activated to different extents by diverse orthosteric ligands and allosteric modulators. However, the mechanisms underlying these variations in signaling activity by allosteric modulators remain largely ...
RCSB PDB - 8UWU: EmrE structure in the proton-bound state …
WEBEmrE structure in the proton-bound state (WT/L51I heterodimer) ... SMR family multidrug efflux protein EmrE: A. 110: Escherichia coli: Mutation(s): 1 Gene Names: emrE: ... Structure Validation. View Full Validation Report. View more in-depth experimental data. Entry History & Funding Information.
RCSB PDB - 7H8I: Group deposition for crystallographic fragment ...
WEBGroup deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z362772344 (CHIKV_MacB-x1194)
RCSB PDB - 8W04: Crystal structure of DUF1735-domain …
WEBCrystal structure of DUF1735-domain containing protein (GH18-like) from Bacteroides faecium at 2.9 A resolution (Space group P21) ... Structure Validation. View Full Validation Report. View more in-depth experimental data. …
RCSB PDB - 9F40: Crystal structure of the NTD domain from S.
WEBCrystal structure of the NTD domain from S. cerevisia Niemann-Pick type C protein NCR1 with ergosterol bound. ... SF-Tool; Ligand Expo; MAXIT; Validate Data; Validation Server; Validation API; ... Structure Validation. View Full Validation Report. Ligand Structure Quality Assessment .
RCSB PDB - 8K70: Structural basis for the distinct roles of non ...
WEBSF-Tool; Ligand Expo; MAXIT; Validate Data; Validation Server; Validation API; ... p50RhoGAP is a key protein that interacts with and downregulates the small GTPase RhoA. p50RhoGAP is a multifunctional protein containing the BNIP-2 and Cdc42GAP Homology (BCH) domain that facilitates protein-protein interactions and lipid binding …
RCSB PDB - 9B0K: INF2 in the Middle of F-Actin (Down state)
WEBMacromolecule Content. Total Structure Weight: 350.49 kDa ; Atom Count: 23,896 ; Modelled Residue Count: 3,020 ; Deposited Residue Count: 3,100 ; Unique protein chains: 2
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