Tools   Select Another Resource Report Type

http://pdbml.pdb.org/

Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available.

Proper citation: Protein Data Bank Markup Language (RRID:SCR_005085) Copy   

•   Source: SciCrunch Registry

http://ligand-expo.rutgers.edu/

An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.

Proper citation: Ligand Expo (RRID:SCR_006636) Copy   

•   Source: SciCrunch Registry

http://polbase.neb.com/

Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software.

Proper citation: Polbase (RRID:SCR_006107) Copy   

•   Source: SciCrunch Registry

http://www.csardock.org

Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data.

Proper citation: Community Structure-Activity Resource (RRID:SCR_002206) Copy   

•   Source: SciCrunch Registry

http://dockground.bioinformatics.ku.edu/

Data sets, tools and computational techniques for modeling of protein interactions, including docking benchmarks, docking decoys and docking templates. Adequate computational techniques for modeling of protein interactions are important because of the growing number of known protein 3D structures, particularly in the context of structural genomics. The first release of the DOCKGROUND resource (Douguet et al., Bioinformatics 2006; 22:2612-2618) implemented a comprehensive database of cocrystallized (bound) protein-protein complexes in a relational database of annotated structures. Additional releases added features to the set of bound structures, such as regularly updated downloadable datasets: automatically generated nonredundant set, built according to most common criteria, and a manually curated set that includes only biological nonobligate complexes along with a number of additional useful characteristics. Also included are unbound (experimental and simulated) protein-protein complexes. Complexes from the bound dataset are used to identify crystallized unbound analogs. If such analogs do not exist, the unbound structures are simulated by rotamer library optimization. Thus, the database contains comprehensive sets of complexes suitable for large scale benchmarking of docking algorithms. Advanced methodologies for simulating unbound conformations are being explored for the next release. The Dockground project is developed by the Vakser lab at the Center for Bioinformatics at the University of Kansas. Parts of Dockground were co-developed by Dominique Douguet from the Center of Structural Biochemistry (INSERM U554 - CNRS UMR5048), Montpellier, France.

Proper citation: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING (RRID:SCR_007412) Copy   

•   Source: SciCrunch Registry

https://www.aideepmed.com/BioLiP/

Semi-manually curated database for biologically relevant ligand-protein binding interactions. Structure data are collected primarily from Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. Database used for serving needs of ligand-protein docking, virtual ligand screening and protein function annotation.BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes, integrates structural alignment algorithms with structure prediction techniques, which enables composite protein structure and sequence-based searching.

Proper citation: BioLiP (RRID:SCR_027685) Copy   

•   Source: SciCrunch Registry

http://www.emdataresource.org/

Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.

Proper citation: EMDataResource.org (RRID:SCR_003207) Copy   

•   Source: SciCrunch Registry

http://cossmos.slu.edu/

Database to search through the nucleic acid structures from the Protein Data Bank and examine structural motifs, including (a)symmetric internal loops, bulge loops, and hairpin loops. They have compiled over 2,000 three-dimensional structures, which can now be searched using different parameters, including PDB information, experimental technique, sequence, and motif type. RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop''''s structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is updated weekly.

Proper citation: RNA CoSSMos (RRID:SCR_006120) Copy   

•   Source: SciCrunch Registry

http://www.wwpdb.org/

Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations.

Proper citation: Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) Copy   

•   Source: SciCrunch Registry

https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/balbes/balbes_layout.html

Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement.

Proper citation: BALBES (RRID:SCR_018763) Copy   

•   Source: SciCrunch Registry

http://metallo.scripps.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. Database and Browser containing quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics, and answer questions such as: How many mononuclear zinc-containing sites are five coordinate with X-ray resolution better than 1.8 Angstroms?, and then be able to visualize and manipulate the matching sites. The database also includes enough information to answer questions involving type and number of ligands (e.g. "at least 2 His"), and include distance cutoff criteria (e.g. a metal-ligand distance no more than 3.0 Angstroms and no less than 2.2 Angstroms). This database is being developed as part of a project whose ultimate goal is metalloprotein design, allowing the interactive visualization of geometrical and functional information garnered from the MDB. The database is created by automatic recognition and extraction of metal-binding sites from metal-containing proteins. Quantitative information is extracted and organized into a searchable form, by iterating through all the entries in the latest PDB release (at the moment: September 2001). This is a comprehensive quantitative database, which exists in SQL format and contains information on about 5,500 proteins.

Proper citation: Metalloprotein Site Database (RRID:SCR_007780) Copy   

•   Source: SciCrunch Registry