FEMME database: topologic and geometric information of macromolecules.

FEMME (Feature Extraction in a Multi-resolution Macromolecular Environment: http://www.biocomp.cnb.uam.es/FEMME/) database version 1.0 is a new bioinformatics data resource that collects topologic and geometric information obtained from macromolecular structures solved by three-dimensional electron microscopy (3D-EM). Although the FEMME database is focused on medium resolution data, the methodology employed (based on the so-called alpha-shape theory) is applicable to atomic resolution data as well. The alpha-shape representation allows the automatic extraction of structural features from 3D-EM volumes and their subsequent characterisation. FEMME is being populated with 3D-EM data stored in the electron microscopy database EMD-DB (http://www.ebi.ac.uk/msd/). However, and since the number of entries in EMD-DB is still relatively small, FEMME is also being populated in this initial phase with structural data from PDB and PQS databases (http://www.rcsb.org/pdb/ and pqs.ebi.ac.uk/, respectively) whose resolution has been lowered accordingly. Each FEMME entry contains macromolecular geometry and topology information with a detailed description of its structural features. Moreover, FEMME data have facilitated the study and development of a method to retrieve macromolecular structures by their structural content based on the combined use of spin images and neural networks with encouraging results. Therefore, the FEMME database constitutes a powerful tool that provides a uniform and automatic way of analysing volumes coming from 3D-EM that will hopefully help the scientific community to perform wide structural comparisons.

[1]  W Chiu,et al.  Teaching electron diffraction and imaging of macromolecules. , 1993, Biophysical journal.

[2]  Herbert Edelsbrunner,et al.  On the Definition and the Construction of Pockets in Macromolecules , 1998, Discret. Appl. Math..

[3]  J M Carazo,et al.  The BioImage Database Project: organizing multidimensional biological images in an object-relational database. , 1999, Journal of structural biology.

[4]  Narayanan Eswar,et al.  Structure of the 80S Ribosome from Saccharomyces cerevisiae—tRNA-Ribosome and Subunit-Subunit Interactions , 2001, Cell.

[5]  Rachid Deriche.  Fast Algorithms for Low-Level Vision , 1990, IEEE Trans. Pattern Anal. Mach. Intell..

[6]  J Frank,et al.  Three-dimensional reconstruction of single particles embedded in ice. , 1992, Ultramicroscopy.

[7]  J Martín-Benito,et al.  Analysis of the interaction between the eukaryotic chaperonin CCT and its substrates actin and tubulin. , 2001, Journal of structural biology.

[8]  H. Edelsbrunner,et al.  Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design , 1998, Protein science : a publication of the Protein Society.

[9]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[10]  M. Baker,et al.  Bridging the information gap: computational tools for intermediate resolution structure interpretation. , 2001, Journal of molecular biology.

[11]  B. Gowen,et al.  Structures of unliganded and ATP-bound states of the Escherichia coli chaperonin GroEL by cryoelectron microscopy. , 2001, Journal of structural biology.

[12]  Wei Zhang,et al.  Placement of the Structural Proteins in Sindbis Virus , 2002, Journal of Virology.

[13]  José María Carazo,et al.  Smoothly distributed fuzzy c-means: a new self-organizing map , 2001, Pattern Recognit..

[14]  H. Saibil.  Conformational changes studied by cryo-electron microscopy , 2000, Nature Structural Biology.

[15]  Masahide Kikkawa,et al.  15 Å Resolution Model of the Monomeric Kinesin Motor, KIF1A , 2000, Cell.

[16]  Kenneth H. Downing,et al.  Structure of the αβ tubulin dimer by electron crystallography , 1998, Nature.

[17]  David L. Stokes,et al.  Structure of the calcium pump from sarcoplasmic reticulum at 8-Å resolution , 1998, Nature.

[18]  B. Alberts.  The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists , 1998, Cell.

[19]  M. Radermacher,et al.  Three-dimensional reconstruction from random projections: orientational alignment via Radon transforms. , 1994, Ultramicroscopy.

[20]  K. Henrick,et al.  New electron microscopy database and deposition system. , 2002, Trends in biochemical sciences.

[21]  N Boisset,et al.  Lumbricus terrestris hemoglobin--the architecture of linker chains and structural variation of the central toroid. , 2001, Journal of structural biology.

[22]  S D Fuller,et al.  The first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike. , 1998, Journal of molecular biology.

[23]  Matthew L. Baker,et al.  Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus , 2001, Nature Structural Biology.

[24]  M Tasumi,et al.  Normal vibrations of proteins: glucagon. , 1982, Biopolymers.

[25]  Joachim Frank,et al.  A 9 Å Resolution X-Ray Crystallographic Map of the Large Ribosomal Subunit , 1998, Cell.

[26]  Herbert Edelsbrunner,et al.  Three-dimensional alpha shapes , 1994, ACM Trans. Graph..

[27]  J. Thornton,et al.  PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.

[28]  W. Wriggers,et al.  Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. , 2002, Journal of molecular biology.

[29]  Tosiyuki Noguti,et al.  Collective variable description of small-amplitude conformational fluctuations in a globular protein , 1982, Nature.

[30]  Herbert Edelsbrunner,et al.  Measuring proteins and voids in proteins , 1995, Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences.

[31]  J. Frank,et al.  Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. , 1997, Journal of structural biology.

[32]  James R. Munkres,et al.  Elements of algebraic topology , 1984 .

[33]  M G Rossmann,et al.  X-ray crystallographic structure of the Norwalk virus capsid. , 1999, Science.

[34]  T. Springer,et al.  Structural homology of a macrophage differentiation antigen and an antigen involved in T-cell-mediated killing , 1982, Nature.

[35]  Rachid Deriche,et al.  Using Canny's criteria to derive a recursively implemented optimal edge detector , 1987, International Journal of Computer Vision.

[36]  Ho-Lun Cheng,et al.  Dynamic Skin Triangulation , 2001, SODA '01.

[37]  S Subramaniam,et al.  Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape , 1998, Proteins.

[38]  A Cheng,et al.  Three-dimensional fold of the human AQP1 water channel determined at 4 A resolution by electron crystallography of two-dimensional crystals embedded in ice. , 2000, Journal of molecular biology.

[39]  Andrew E. Johnson,et al.  Using Spin Images for Efficient Object Recognition in Cluttered 3D Scenes , 1999, IEEE Trans. Pattern Anal. Mach. Intell..

[40]  Amarnath Gupta,et al.  Modeling shape and topology of low-resolution density maps of biological macromolecules. , 2002, Biophysical journal.

[41]  S. Harrison,et al.  Structure of the reovirus core at 3.6 Å resolution , 2000, Nature.

[42]  Alfred V. Aho,et al.  The Design and Analysis of Computer Algorithms , 1974 .

[43]  Nikolaus Grigorieff,et al.  Molecular Machines , 2001, The Journal of cell biology.

[44]  H. Edelsbrunner.  The union of balls and its dual shape , 1995 .

[45]  M. Heel,et al.  Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. , 1987 .

[46]  Florence Tama,et al.  Mega-Dalton biomolecular motion captured from electron microscopy reconstructions. , 2003, Journal of molecular biology.

[47]  J. Dubochet,et al.  Cryo-electron microscopy of vitrified specimens , 1988, Quarterly Reviews of Biophysics.

[48]  José María Carazo,et al.  Spin Images and Neural Networks for Efficient Content-Based Retrieval in 3D Object Databases , 2002, CIVR.

[49]  R. Henderson,et al.  Three-dimensional model of purple membrane obtained by electron microscopy , 1975, Nature.

[50]  Yoshinori Fujiyoshi,et al.  [Structure and function of water channels]. , 2002, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

[51]  Jianpeng Ma,et al.  Domain movements in human fatty acid synthase by quantized elastic deformational model , 2002, Proceedings of the National Academy of Sciences of the United States of America.