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Lomonosov MSU's web-sites

Web-sites about proteomics

Web-sites about electron microscopy

Software web-sites

  • BSoft - a software package written for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing.
  • CTFFind & CTFTilt - EM utilities for defocus and astigmatism determination.
  • em2em - a program to convert images from/to many formats used by 3DEM community.
  • EMAN2 - a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images.
  • FReAlign - (Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.
  • ImageJ - ImageJ is a public domain Java image processing program. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images.
  • IMAGIC - a high-end environment for the analysis of images, spectra and other multi-dimensional data-sets. Mostly used for SPA.
  • IMOD - a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial and optical sections.
  • PyMol - widely used molecular visualization package.
  • SerialEM - a program for acquiring tilt series for electron tomography, also automated SPA data collection is now possible.
  • RELION - (REgularised LIkelihood OptimisatioN) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in cryo-EM.
  • Scipion - is an image processing framework that integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions.
  • SIMPLE - (Single-particle IMage Processing Linux Engine) is a program package for cryo-EM image processing, focusing on ab initio 3D reconstruction of low-symmetry single-particles.
  • Situs - a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies.
  • SPARX - (Single Particle Analysis for Resolution eXtension) is a image processing environment with an extensive library of python scripts that perform specific computational tasks.
  • SPIDER - (System for Processing Image Data from Electron microscopy and Related fields) is a large image processing suite for electron microscopy.
  • UCSF Chimera - a highly extensible, interactive molecular graphics program, often a tool of choice for rendering EM volumes.
  • VMD - a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.