This is a compilation of links which are relevant to this Project.
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links for lipids, proteins and membranes

Post by bjoern » 18.07.2006, 13:21

Last Update: 11.11.2016

Avantilipids [2D] [~3D]
  • Avanti Polar Lipids, Inc.
    A commercial page providing lipids. Here formulas and names of lipid (models) can be found. Also MDL Molfiles can be downloaded, but they are not very interesting for 3D puposes.
  • The well-known enzyme database contains also informations about the well-differentiated localization of proteins in different cell components.
    :arrow: Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D (2007).
    BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
    Nucleic Acids Res. 2007 Jan 12;35 Database issue:D511-4.
Chemistry Molecular Models [3D]
  • A very nice collection of many constructed PDB molecule and lipid models maintained by Dr. Tom Zamis at the Department of Chemistry at the University of Wisconsin in Stevens Point. And the only site to my knowledge which contains a nice Sphingomyelin structure (Sphingomyelin.pdb).
  • the UniProt Knowledgebase (Swiss-Prot and TrEMBL)
    dedicates itself to the analysis of protein sequences and structures, relevant for the search of proteins and cellular components
    :arrow: Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31:3784-3788(2003)
  • Hetero-compound Information Centre - Uppsala
    contains segments of PDB files (e.g. a lipid - PC2) needed for the modelling of a membrane and the localization of proteins in the cell, for complete proteins refer to the RCSB PDB
    :arrow: Kleywegt GJ, Jones, TA (1998). Databases in protein crystallography. Acta Cryst D54, 1119-1131 (CCP4 Proceedings)
  • One of the reference pathway databases provides also lipid pathways, and of course it offers also the 2D structures of lipids with links to LIPIDMAPS, PubChem etc..
    :arrow: Hashimoto K, Tokimatsu T, Kawano S, Yoshizawa AC, Okuda S, Goto S, Kanehisa M (2009). Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr. Res. 344, 881-887.
Klotho [3D]
Only available archived at: ... rg/klotho/
  • Biochemical Compounds Declarative Database
    A collection of rare synthesized proteins like the sphingomyelin.PDB.
    :arrow: Klotho : Biochemical Compounds Declarative Database
    Cannon B, SadekarS , Taylor D, Dunford-Shore BH, Sulaman W, Feng B, Fabrizio F, Holcomb J, Wise W, Kazic T (1994). 1994--present.
    Klotho: Biochemical Compounds Declarative Database
  • Information about lipid pathway maps, structures in 2D and lipid properties. Establishing an elaborated lipid nomenclature.
    :arrow: Fahy E, Subramaniam S, Murphy R, Nishijima M, Raetz C, Shimizu T, Spener F, van Meer G, Wakelam M, Dennis E (2009). Update of the LIPID MAPS comprehensive classification system for lipids. Journal of Lipid Research 50, S9-S14.
LipidBank [2D]
  • Search for 3000 molecular structures of lipids. Not very up-to-date anymore, last update is from 2007.
    :arrow: Watanabe K, Yasugi E, Oshima M (2000). How to search the glycolipid data in LIPIDBANK for Web: the newly developed lipid database. Japan Trend Glycosci. and Glycotechnol. 12, 175-184.
LipidBook [3D]
  • Contains a set of force field parameters for lipids, detergents, and similar molecules with a special focus on membrane modeling. There are also some PDB structures included.
    :arrow: Domański J, Stansfeld P, Sansom MSP, Beckstein O (2010). Lipidbook: A Public Repository for Force Field Parameters Used in Membrane Simulations. J. Membrane Biol. 236, 255-258.
  • Sorts all lipids according their types.
    contains abstracts of many publications, e.g. relevant for cell biology
OPM [3D]
  • Oriantations of Proteins in Membranes database
    contains the orientation of proteins between the membrane layers
    :arrow: Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006). OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625.
  • Protein Data Bank of Transmembrane Proteins
    contains at the moment ca. 600 transmembrane structures, but there is no adequate search-utility implemented yet
    :arrow: Tusnády GE, Dosztányi Z, Simon I (2005). Bioinformatics 20, 2964-2972; Nucleic Acids Research 33 Database Issue, D275-8

PubChem Compound [2D] [~3D]
  • PubChem can be searched for lipids, containing 2D and sometimes also 3D/conformer structures. It is also possible to search explicitly for conformers. But there is no direct PDB export, so converters are needed.
    :arrow: Bolton EE, Wang Y, Thiessen PA, Bryant SH (2008). Annual reports in computational chemistry 4, 217-241

  • the PDB database
    contains complete PDBs consisting of different PDB segments, for extrated segments please refer to the HIC-UP
    :arrow: Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000). The Protein Data Bank. Nucleic Acids Research, 28, 235-242

WebQC Molecular Format converter [2D] [3D] :idea: NEW
  • You want to convert e.g. a MOL file to PDB file and you also forgot which program on which OS you used for this purpose three years ago? Here is the solution! The website also contains a set of other interesting tools with focus on chemistry (please deactivate Ad blockers to keep this website alive!)
    :arrow: Molecular formats converter,, 11/11/2016

:arrow: marks the cite-remark used in publications

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