ABSTRACT
In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this wide-reaching change is the continuous development of image processing software. Here we present Scipion, a software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from http://scipion.cnb.csic.es.
Subject(s)
Algorithms , Image Processing, Computer-Assisted/methods , Imaging, Three-Dimensional/instrumentation , Microscopy, Electron/methods , Imaging, Three-Dimensional/methods , Reproducibility of Results , WorkflowABSTRACT
With the advent of high throughput techniques like Next Generation Sequencing, the amount of biological information for genes and proteins is growing faster than ever. Structural information is also rapidly growing, especially in the cryo Electron Microscopy area. However, in many cases, the proteomic and genomic data are spread in multiple databases and with no simple connection to structural information. In this work we present a new web platform that integrates EMDB/PDB structures and UniProt sequences with different sources of protein annotations. The application provides an interactive interface linking sequence and structure, including EM maps, presenting the different sources of information at sequence and structural level. The web application is available at http://3dbionotes.cnb.csic.es.
Subject(s)
Proteomics/statistics & numerical data , Software , Adenomatous Polyposis Coli Protein/chemistry , Adenomatous Polyposis Coli Protein/genetics , Adenomatous Polyposis Coli Protein/metabolism , Amino Acid Sequence , Antigens, CD , Base Sequence , Cadherins/chemistry , Cadherins/genetics , Cadherins/metabolism , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Databases, Protein , F-Box Proteins/chemistry , F-Box Proteins/genetics , F-Box Proteins/metabolism , Gene Expression , Humans , Internet , Models, Molecular , Protein Conformation , Proto-Oncogene Proteins p21(ras)/chemistry , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/metabolism , Structure-Activity RelationshipABSTRACT
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.