World Index of BioMolecular Visualization Resources

Molecules: Sources of PDB Files

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  3D Molecular Modeling Homepage:
Hundreds of pharmaceutical organic compounds may be viewed in Chime. The atomic coordinate files are in MOL format and may be downloaded by clicking on MDL to raise Chime's menu, then File, Save Molecule As. Also available for each compound is a simulation of thermal motion; these may be downloaded as XYZ files.        

  Atlas of Macromolecules:
Browsable short descriptions and links to over 70 PDB files. PDB ID codes are listed. Clicking a link displays the molecule in Protein Explorer. The Atlas is divided into over a dozen sections, such as enzymes, soluble proteins, structural proteins, integral membrane proteins, DNA/RNA, proteins complexed to nucleic acids, whole virus capsids, anthrax toxins, immuno-molecules, carbohydrates, unusual tertiary/quaternary structures, and "magnificent molecular machines". Small screenshots decorate the Atlas. Nominations of molecules to include in the Atlas are welcome.   

  ChemDB at UC Irvine:
A database containing over four million small organic compounds. Find a chemical by basic criteria like molecular weight and predicted logP, or by the more abstract notion of structural similarity.

Comment by Eric Martz, November 2005: I could not find a tutorial. Here is one way to find a 3D structure. Enter the Chemical Search. Under Similarity Search, click on Sketch. Use the interface to sketch all or part of the molecule you want. Click Submit. Click the Search button. In the results list, click on the hyperlinked 2D image, or the SMILES string. A new page appears that includes the 3D structure in Jmol. Use the pull-down menu to select a file format, e.g. PDB. Click the Download Chemical button.

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  Chemfinder:
75,000 small molecules. When you find a molecule, look near the bottom of the page for the link to "This compound in PDB format".

  ChemViz:
For those who have Chime (www.mdlchime.com) installed, ChemViz provides a free source of atomic coordinate files for small molecules, in PDB format, from the Cambridge Structural Database (CSD). After registering for your free account, use the CSD button to do a search. If your search is successful, using the default "Render Selection", press Submit, and the molecule will appear in Chime. Click on MDL to pop-up Chime's menu, selecting File, Save Molecule As. Warning: at the time of this writing (October, 2001) the database options pdb and both don't work -- they always give zero hits. This was confirmed by the webmaster. Use only the default CSD database!

  Combinatorial Extension: Databases and Tools for 3-D Protein Structure Comparison and Alignment:
The Combinatorial Extension (CE) site performs two important functions that return PDB files:

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  CORINA: 1000 3D Structures Free:
This website will calculate a 3D structure for small organic molecules free. The compound must be entered with a JAVA molecular editor, or as a SMILES string. The results will appear in a JAVA viewer, and can be downloaded as a PDB file. For more information, visit CORINA (COoRdINAtes).

  Crystal Lattice Structures, Inorganic:
Inorganic crystal lattice structures are available from the Complex Systems Theory Branch, Code 6690 of the Naval Research Laboratory. Their page "currently contains links to 92 structures in 41 of the 230 space groups"(as of 12/1/00). Selected examples of these can be viewed through Chime at Andrew Maverick's crystal page, which also includes a link to the PDB files for each crystal.

  Crystallography Open Database:
Empirical and theoretical structures for more than 18,000 inorganic crystals and small organic compounds. Visitors can upload new data entries. All data on this site have been placed in the public domain by the contributors. Data are in crystallographic information format (CIF, not PDB).  
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  DNA Tools: Model.It:
Model.It is one of the DNA Tools offered here. You can submit the sequence for a DNA strand, and receive coordinates for straight A or B form DNA double helix, with the complementary strand automatically supplied. Important: If you have MDL Chime installed, you will see a blank black Chime. Go ahead and use Chime's menu (File, Save Molecule As) and the coordinates will be saved in PDB format. Subsequently they can be loaded into e.g. Protein Explorer and visualized.  

  Entrez Search and Retrieval System of NCBI:
A single query will retrieve not only matching atomic coordinate files, but also sequences, medical literature references, genome references, and taxonomy references. The 3D Structure section accepts queries by name or sequence (protein or nucleotide). For a particular hit, a search for closely related records can be done automatically, without formulating a query manually.

  EXLNT: Search tools for a database of 3-D Structures of Protein and DNA:   (English; French; Spanish; German; Swedish; Russian )

A searchable database of information on sequence, hetero atoms, motifs and structural class extracted from the PDB, SCOP and PROSITE.

PDB        AC              DO              EC
1fbl   PS00546    PDOC00472       EC:3.4.24.7 KEGG WIT      Fibroblast (Interstitial) Collagenase (Mmp-1    
1hfc   PS00546    PDOC00472       EC:3.4.24.7 KEGG WIT      Fibroblast Collagenase (E.C. 3.4.24.7) - Cha    
1mmp   PS00546    PDOC00472       EC:3.4.24.23 KEGG WIT     Matrilysin      
2aig   PS00142    PDOC00129       EC:3.4.24.46 KEGG WIT     Peptidomimetic Inhibitor Pol647 
2ayk   PS00546    PDOC00472       EC:3.4.24.7 KEGG WIT      Collagenase     
 
1a1g MERPYACPVESCDRRFSDSSNLTRHIRIHTGQKPFQCRIC  Dsnr Zinc Finger Peptide 
1ard RSFVCEVCTRAFARQEHLKRHYRSHTNEK  Yeast Transcription Factor Adr1 (Residues 102 
1bbo LKKHIRTHTDVRPYHCTYCNFSFKTKGNLTKHMKSKAHSK  Human Enhancer-Binding Protein Mbp-1 Muta 
1bhi MSDDKPFLCTAPGCGQRFTNEDHLAVHKHKHEMTLKFG  Cre-Bp1 
Example queries: Kinases; Kinases of human origin; Kinases of human origin with bound nucleotide ...

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  ExPDB (single chains from PDB files):
This on-line utility allows you to get any single protein chain from a PDB file and save it to disk. Non-protein chains are not provided, and water and most covalently or noncovalently bonded hetero atoms are removed from protein chains.  

  Finding Structures on the IUMSC Data Server:
Empirically determined atomic coordinate files for over 2,000 inorganic compounds and crystals. These are downloadable in CRT format. A free utility for converting CRT to PDB format for viewing in Chime or RasMol is available.   

  HIV Protease Structures Database:
The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage. It serves a global community of researches, educators and students.

The structures contained in HIVdb have either been officially deposited to the Protein Data Bank (PDB), or have been obtained directly from depositors for HIVdb only. In the latter case, they may have been less completely refined, or even not refined at all beyond the placement of the ligand; or they may have resulted from experiments that were never fully completed and published, but nevertheless be comparable in quality to the structures deposited in PDB. The structures unique to HIVdb came mostly from pharmaceutical companies and were used primarily as intermediate steps of drug design, in which full refinement was not advisable for the lack of need and resources.

 
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  Interactive Biochemistry - Garrett & Grisham: PDB Files:
Links to hundreds of molecules covered in the Garrett & Grisham biochemistry textbook. Clicking a link displays the molecule in Chime, from which the PDB file can be saved to disk if desired, using Chime's menu. The list is organized by chapters in the textbook.   

  KLOTHO: Biochemical Compounds Declarative Database:
PDB files for over 800 biochemicals, including amino acids, vitamins, lipids, hormones, sugars, bases nucleosides and nucleotides, and metabolic intermediates.  

  Lipid Bilayer Membranes:
PDB files for crystalline phosphatidyl choline bilayers constructed from theory and after molecular dynamics simulations in gel- and fluid-like conformations (100 phospholipids per leaflet plus water). Snapshots of RasMol views are also available here. A RasMol "movie" script on lipid bilayers that explains these can be downloaded. (I am willing to pay a qualified person to port this to a Chime presentation -- contact me if interested.) The movie script also includes a model of the gramicidin channel in a hydrated phosphatidyl ethanolamine bilayer (Serge Crouzy, Thomas B. Woolf, and Benoit Roux, "A molecular dynamics study of gating in dioxolane-linked gramicidin A channels", Biophys. J. 67:1370-86, 1994).

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  Lipid micelle and bilayer PDB files:
PDB files are downloadable for theoretical models of hydrated phosphatidyl choline micelles, hydrated lipid bilayers, and alamethicin helix bundles (a channel?).  

  MDDNA: Construct Detailed DNA Models:
In reality, the DNA is not a perfectly straight helical structure but instead presents structural properties that dependent on the sequence composition. MDDNA is a web-based tool to study and model the fine structural details of DNA on the basis of data extracted from a large set of molecular dynamics (MD) trajectories of DNA sequences involving all the unique tetranucleotides. The dynamic web interface can be employed to analyze the first neighbor sequence context effects on the 10 unique dinucleotide steps of DNA. Functionality is included to build all atom models of any user-defined sequence based on the MD results. Atomic model of the DNA structure is generated in PDB format which can be viewed online in JMol or downloaded. The backend of this server comprises of a relational database system storing the conformational details of all the 136 unique tetranucleotide steps derived from MD simulations.

Another program 3DNA (http://rutchem.rutgers.edu/~xiangjun/3DNA/) is available to build DNA models. Note: "DNA Tools: Model It" is another site in this compendium of websites capable of generating DNA structures based on "di and tri" nucleotide building blocks data derived from gel mobility, X-ray and NMR structural information. The structures constructuted by MDDNA are based on a more information rich "tetra" nucleotide building block, albeit based on computer simulation results. MDDNA supports the JMol applet to directly load the constructured DNA structure in your web page.

The PSC Web Tools (temporarily unavailable and under development, Nov 2006) also provides features to constructure DNA structures. But it is restricted to constructing straight canonical A and B form structures, lacking the sequence dependent structural detail that can be derived from MDDNA or Model It.

  Membrane Channel & Pump Structures:
An index table of structures for biochemistry courses. PubMed entries and Chime displays of the structures can be viewed by following the links provided. (PDB ID) for the structures displayed are shown above.

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  Molecular database without transition elements:   (English, French )
Fifty files with the pdb format that describe the geometric characteristics of simple inorganic molecules. Theses files were made with the atom's coordinates to respect the experimental values. So, theses files permit the illustration of classical geometries learnt in the VSEPR method

  Molecular Models from Chemistry at Okanagan University College:
The premier source of PDB files for organic compounds. Over 1,300 available.  

  NCI Database Browser V2:
Nearly 250,000 compounds from the US National Cancer Institute, with 3D structures calculated by CORINA and MSI Catalyst. Now includes additional 3D export formats and 3D search functionality. The browser is designed for professional chemists -- expect to spend a while figuring out how to use it. Read the help!  
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  OCA Browser:
The OCA Browser can find some things that can't be found with SearchFields. For example, entries with active site information can be found in OCA by searching for site_identifier. OCA also has fields for Kingdom, Gene, Disease, and Function. On the other hand, SearchFields can find some things more easily than OCA. For example it can limit searches to entries which contain coordinates for RNA but neither protein nor DNA, and it can find "phospholipase C" while OCA ignores the "C". The OCA database is updated weekly with the latest releases, and there are mirror sites on several continents. OCA is an enhanced version of the browser that was available from the former PDB at Brookhaven National Laboratory.  

  PDB At A Glance:
Look up molecules in an alphabetized list of over 20 major categories, such as antibiotics, calcium-binding proteins, enzymes, immune system molecules, membrane-associated proteins, signaling molecules, toxins. Under most categories are subcategories, for example under enzymes are hydrolases, isomerases, lyases, proteases, transferases, etc. Under each of these are sub-subcategories, for example under hydrolases (non-protease) are acetylcholinesterase, endonucleases, glycosidases, heat shock proteins, lipases, phosphatases, etc. Under each of the most specific categories, molecules are grouped according to whether they are uncomplexed, complexed, complexed with an inhibitor, or represent a non-complexed inhibitor or activator. A resource provided by the NIH Center for Molecular Modeling (under Databases).

  PDB Files for Teaching Biochemistry:
This site contains PDB files of chemical and biochemical structures that the typical undergraduate chemistry student may use in his or her academic career. It is intended for both the student and instructor in the chemical and biochemical sciences. Structures in the following categories are freely available: amino acids, nucleic acids, cofactors, classic proteins (e.g. hemoglobin), nucleic acid binding proteins, Krebs cycle enzymes, gluconeogenesis and glycolysis, photosynthesis.

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  PDB Lite:
PDB Lite is a search interface designed for students, educators, and scientists who search for atomic coordinate files only occasionally. PDB Lite differs from SearchLite in the following ways: Jargon is avoided or explained, and crystal technicalities are omitted. Synonyms are expanded automatically ("hemoglobin" finds "haemoglobin"). A checkbox option finds only sequence non-redundant structures, useful in cases where there are too many hits. Findings are tabulated with aligned columns easier to scan than the comparable list at RCSB. Entering a query that won't work produces a warning with an explanation of how to rephrase the query. Step-by-step instructions are offered for saving PDB files in Windows or Macintosh, so you can successfully open it in Protein Explorer, RasMol, Deep View, etc. The database is updated weekly with the latest releases, and mirror sites are available on several continents.

  Pherobase:
The world's largest database of behavior-modifying chemicals, Pherobase enables you to find insect pheromones by taxon, application, or chemistry. Over 3,000 compounds are included, with literature citations. Each pheromone is shown in a traditional 2-D drawing, as well as in 3-D with the MDL Chime plugin (from which you can download the atomic coordinates or PDB file for any compound shown). The author, Ashraf M. El-Sayed, works at HortResearch New Zealand, which sponsors this free site.

  Probable Quaternary Structures:
Probable Quaternary Structures (PQS) offers full biological or functional units (as PDB-formatted data files ending ".mmol"), completed with symmetry operations. PQS also provides an analysis of whether inter-chain protein contacts are likely to be present in the functional molecule, or are merely artifacts of crystallization. The original atomic coordinate file from a crystallographic experiment contains the minimal asymmetric unit, often only part of the biological unit. For example, although hemoglobin is a tetramer, 1hho contains only a dimer; PQS offers 1hho.mmol completed to the tetramer. PQS offers completed virus capsids, for example, the 31 megabyte polio capsid, 2plv.mmol. In cases where the original PDB files contains artifactual, crystallization-induced oligomers, PQS offers the monomer. This site can also pick and the best single model (or any specified model) from an NMR ensemble, and offer it for download.

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  Protein Data Bank:
The Protein Data Bank is the internationally recognized single respository of all published macromolecular three-dimensional structures determined empirically. It offers two search interfaces, SearchLite and SearchFields. Atomic coordinate data files can be downloaded in PDB or mmCIF formats. New releases are added once each week, and are immediately made available for updating alternative search interfaces such as OCA and PDB Lite.

  PSC Web Tools: Generate DNA/RNA PDB from sequence:
Here you can enter a strand sequence, and immediately receive a modeled PDB file for DNA or RNA in A form, or DNA in B form. The only constraint is that only standard B-form (or A-form) PDB files are generated, and these contain only the imino hydrogens, i.e. Watson-Crick base pairing hydrogens -- all other hydrogen atoms are missing. Site courtesy of the Pittsburgh Supercomputer Center.    

  Simple, Common, and Interesting Molecules:
Molecules available here can be viewed in the locally authored Java Molecule Modeler applet, or in Chime (from which the PDB file can be downloaded with Chime's menu: click on MDL, File, Save Molecule As). This site excels at inorganic compounds: over a dozen minerals, boron and boranes, sulfur-eight, and several forms of carbon including buckyballs. Included are a handful of "Molecules of Biological Significance to Humans", mostly hormones. Also "Molecules of Environmental Importance", all 20 amino acids and 5 nucleotides, several poisons, vitamins and drugs. Over a dozen simple organic compounds are available.

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  Structural Classification of Proteins (SCOP):
Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.

Proteins are classifed into Classes such as alpha, beta, mixed, membrane and cell surface, small, coiled-coil. Under each Class are Folds, Superfamilies, and Families. For example, Staphylococcal protein A is classified as follows:

  1. Root: scop
  2. Class: All alpha proteins
  3. Fold: Bacterial immunoglobulin/albumin-binding domains
    3 helices; bundle, closed, left-handed twist; up-and-down
  4. Superfamily: Bacterial immunoglobulin/albumin-binding domains
  5. Family: Immunoglobulin-binding protein A modules
Each item in the above list is hyperlinked. Under such a classification are a list of the included PDB ID codes linked to downloading and viewing options.

  Structures of Small Molecules & Building Blocks:
Dozens of small molecules are displayed in Chime. You can download the PDB atomic coordinate file for any one you are looking at by clicking on Chime's "MDL" frank (lower right corner), then on the menu that pops up, File, Save Molecule As. Includes miscellaneous ionic and polar neutral compounds, amino acids, nucleotides, fatty acids, cholesterol, phospholipids, and mono- and disaccharides.

  SWEET:
SWEET - A Web-based Carbohydrate Builder
Sweet is a WWW-based tool which rapidly converts the commonly used carbohydrate sequence information directly into a preliminary but reliable 3D model which can be visualised and written to files in several ways.
   
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  Vector Alignment Search Tool (VAST):
Given a 3D structure as a query (your own or a PDB ID code), VAST will find similar structures, without regard to sequence similarity. You can get a PDB file containing the two molecules aligned.        
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Visitor-Maintained Index programming by Trevor D. Kramer.