Structural Biotechnology Group

Bioengineering department at Lomonosov Moscow State University

• Home
• News
  • News archive
• Research
  • Projects
  • Collaboration
  • Facilities
• People
• Publications
  • 2023
  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012
  • 2011
  • 2010
  • 2009
  • 2008
  • Before 2008
• Seminars
• Media
  • Protocols & methods
  • Thesises
  • Gallery
  • struct3D
• Links
• Contacts

Links

Lomonosov MSU's web-sites

• MSU official web-site
• MSU Biological Faculty official web-site
• Bioengineering Department
• Website of the Department of Bioengineering, Biological Faculty MSU
• Supercomputers "Lomonosov", "Lomonosov-2", Chebyshev" and "GraphIT" at Research Computer Center
• Unique installment Three-dimensional electron microscopy and spectroscopy

Web-sites about proteomics

• SWISS-2D database for 2D electrophoresis

Web-sites about electron microscopy

• Database of 3D-ЕМ structures
• Caltech EM video course of prof. Grant Jensen
• Collaborative Computational Project for Electron cryo-Microscopy
• 3DEM mailing list: news, links, conferences etc.
• Electron microscopy for dummies
• LMB EM course 2014

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.