World Index of BioMolecular Visualization Resources
Molecules: Sources of PDB Files
Titles
Subjects
Authors:
Detailed
Compact
HOME
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Anonymous, names of creators prohibited from website by NRL policy
(cst-www.nrl.navy.mil
)
- Crystal Lattice Structures, Inorganic
Description
(Cross-indexing terms:
lattices of inorganic crystals; inorganic crystal lattices)
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Anonymous, PSC
(www.psc.edu
)
- PSC Web Tools: Generate DNA/RNA PDB from sequence
Description
(Cross-indexing terms:
DNA model from sequence; RNA model from sequence)
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Baldi, PIerre
(cdb.ics.uci.edu
)
- ChemDB at UC Irvine
Description
(Cross-indexing terms:
small molecules; organic compounds; Jmol)
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Berman, Helen
(www.rcsb.org
)
- Protein Data Bank
Description
(Cross-indexing terms:
mmCIF; SearchLite; SearchFields)
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Biotechnology Information, National Center for
(www.ncbi.nlm.nih.gov
)
- Entrez Search and Retrieval System of NCBI
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Bohne, Andreas
(www.dkfz.de
)
- SWEET
Description
(Cross-indexing terms:
Carbohydrates, 3D-Model PDB calculated from sequence)
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Cambridgesoft, Inc.
(www.chemfinder.com
)
- Chemfinder
Description
(Cross-indexing terms:
organic compounds; drugs; metabolites; sugars)
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ChemViz, NCSA
(chemviz.ncsa.uiuc.edu
)
- ChemViz
Description
(Cross-indexing terms:
organic compounds; drugs; metabolites; small molecules; Cambridge Structural Database)
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Dixit, Surjit
(humphry.chem.wesleyan.edu
)
- MDDNA: Construct Detailed DNA Models
Description
(Cross-indexing terms:
DNA Structures from sequences; Molecular Dynamics Models of DNA; Jmol)
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Dobashi, Akira
(www.pharmis.org
)
- 3D Molecular Modeling Homepage
Description
(Cross-indexing terms:
drugs, hundreds; pharmaceuticals, hundreds; XYZ animations of thermal motion of drugs, hundreds; animations of thermal motions of drugs, hundreds)
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Dupuis, Gerard
(www.faidherbe.org
)
- Molecular database without transition elements
Description
(English, French)
(Cross-indexing terms:
VSEPR; inorganic compounds)
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El-Sayed, Ashraf M.
(www.pherobase.com
)
- Pherobase
Description
(Cross-indexing terms:
pheromones; insect pheromones; behavior-modifying compounds)
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Garrett, R. H.
(www.brookscole.com
)
- Interactive Biochemistry - Garrett & Grisham: PDB Files
Description
(Cross-indexing terms:
amino acids; sugars; metabolites; nucleotides; nucleic acids; enzymes; proteins)
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Harden, Don
(chemistry.Gsu.EDU
)
- PDB Files for Teaching Biochemistry
Description
(Cross-indexing terms:
amino acids; nucleic acids; cofactors; gluconeogenesis; glycolysis; photosynthesis)
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Henrick, Kim
(pqs.ebi.ac.uk
)
- Probable Quaternary Structures
Description
(Cross-indexing terms:
biological units; capsids, viral, complete; virus capsids, complete; functional units; European Bioinformatics Institute Probable Quaternary Structures; NMR, best or any single model; model, best or single from NMR ensemble)
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Huffman, John C.
(www.reciprocalnet.org
)
- Simple, Common, and Interesting Molecules
Description
(Cross-indexing terms:
hormones; pesticides; poisons; amino acids; nucleotides; inorganic compounds; organic compounds; elements; buckyballs; carbon; boron and boranes)
- Finding Structures on the IUMSC Data Server
Description
(Cross-indexing terms:
inorganic compounds and crystals; crystals, inorganic)
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Ihlenfeldt, Wolf-D.
(www2.chemie.uni-erlangen.de
)
- CORINA: 1000 3D Structures Free
Description
(Cross-indexing terms:
new structures, calculate your own free; calculation of new structures free; computation of new structures, free)
- NCI Database Browser V2
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Kazic, Toni
(www.biocheminfo.org
)
- KLOTHO: Biochemical Compounds Declarative Database
Description
(Cross-indexing terms:
vitamins; sugars; bases; nucleosides; nucleotides; energy metabolites; metabolic compounds; amino acids; lipids; hormones)
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Madej, T.
(www.ncbi.nlm.nih.gov
)
- Vector Alignment Search Tool (VAST)
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Martz, Eric
(www.pdblite.org
)
- PDB Lite
Description
(Cross-indexing terms:
student search interface; saving PDB files to disk, instructions for Windows and Macintosh; non-redundant structures; search interface for beginners or nonspecialists; find PDB files, for students, educators, nonspecialists)
- Lipid Bilayer Membranes
Description
(Cross-indexing terms:
membranes; phospholipid bilayers; bilayers, lipid; gramicidin channel in lipid bilayer; channel, ion, in lipid bilayer)
- Atlas of Macromolecules
Description
(Cross-indexing terms:
enzymes; soluble proteins (non enzymatic); structural proteins; membrane proteins, integral; DNA/RNA; virus capsid, SV40; anthrax toxins; toxins, anthrax; immuno-molecules; carbohydrates; unusual secondary/tertiary structures; magnificent molecular machines)
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McClure, William
(www.bio.cmu.edu
)
- Membrane Channel & Pump Structures
Description
(Cross-indexing terms:
KcsA K+ Channel (1k4c.pdb); MthK K+ Channel (1lnq.pdb); KvAP, a Voltage-Gated K+ Channel (1orq.pdb, 1ors.pdb); KirBac1.1 K+ Channel (1p7b.pdb); EcClC Chloride Channel (1ots.pdb, 1otu.pdb); E. coli Glycerol Channel (1fx8.pdb, 1ldi.pdb); AQP1 Aquaporin Channel (1j4n.pdb); MscS, Mechanosensitve Small Conductance Channel (1mxm.pdb); MscL, Mechanosensitve Large Conductance Channel (1msl.pdb); Ionophores: Gramicidin & Valinomycin; SERCA1 Ca2+ Pump (1eul.pdb, 1iwo.pdb); Bacteriorhodopsin (1c3w.pdb, 1dze.pdb))
- Structures of Small Molecules & Building Blocks
Description
(Cross-indexing terms:
nucleotides; sugars; monosaccharides; disaccharides; fatty acids; cholesterol; phospholipids; amino acids)
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Meek, James
(exlnt.com
)
- EXLNT: Search tools for a database of 3-D Structures of Protein and DNA
Description
(English; French; Spanish; German; Swedish; Russian)
(Cross-indexing terms:
SCOP; PROSITE; KEGG; WIT; Command line; Sequence display; Francais; Deutsch; Svenska; Russian; Espagnol; pattern; command-line; motif.)
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Murzin, Alexey G.
(scop.mrc-lmb.cam.ac.uk
)
- Structural Classification of Proteins (SCOP)
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Pearlstein, R.
(cmm.info.nih.gov
)
- PDB At A Glance
Description
(Cross-indexing terms:
Categories and subcategories of molecules; alphabetic list of molecules)
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Peitsch, Manuel C.
(www.expasy.ch
)
- ExPDB (single chains from PDB files)
Description
(Cross-indexing terms:
single protein chain from any PDB file; one protein chain from any PDB file; chains, protein, one at a time, from any PDB file)
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Prilusky, Jaime
(bioinfo.weizmann.ac.il
)
- OCA Browser
Description
(Cross-indexing terms:
active sites; site_identifier, finding entries with; Brookhaven browser)
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Shindyalov, Ilya N.
(cl.sdsc.edu
)
- Combinatorial Extension: Databases and Tools for 3-D Protein Structure Comparison and Alignment
Description
(Cross-indexing terms:
aligning protein chains; structure searching regardless of sequence)
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Team, Crystallography Open Database
(www.crystallography.net
)
- Crystallography Open Database
Description
(Cross-indexing terms:
cif data; inorganic crystals; organic compounds, small; public domain atomic coordinates)
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Tieleman, D. Peter
(indigo1.biop.ox.ac.uk
)
- Lipid micelle and bilayer PDB files
Description
(Cross-indexing terms:
alamethicin helix bundles; micelles, lipid; bilayers, lipid)
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Vlahovicek, Kristian
(hydra.icgeb.trieste.it
)
- DNA Tools: Model.It
Description
(Cross-indexing terms:
DNA model from sequence)
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Vondrasek, Jiri
(srdata.nist.gov
)
- HIV Protease Structures Database
Description
(Cross-indexing terms:
HIV protease inhibitors; proteases and inhibitors; SIV; immunodeficiency virus; drug resistance)
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Woodcock, Dave
(www.molecularmodels.ca
)
- Molecular Models from Chemistry at Okanagan University College
Description
(Cross-indexing terms:
Organic compounds (over 1,300!), indexed and searchable; alcohols; amines; esters; ketones; alkanes; alkenes; alkynes; aldehydes; ethers; nitro compounds; aromatics; halogenated compounds; phenols; drugs; food colors; flavors; aromas; acids, organic; chiral molecules; inorganic molecules (23 cases); cyclic molecules; natural products; poisons)
32 total first authors.
Visitor-Maintained Index
programming by Trevor D. Kramer.