Flex-EM – Fitting and Refinement of Atomic Structures

Flex-EM

:: DESCRIPTION

Flex-EM includes a rigid fitting stage followed by a refinement stage. Rigid fitting can be performed with Mod-EM or any other rigid fitting methods. The refinement stage starts with the components rigidly fitted in the approximate positions in the map. Two methods are available: conjugate gradients minimization (CG) and simulated annealing molecular dynamics (MD).

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Flex-EM

:: MORE INFORMATION

Citation

M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, A. Sali.
Protein Structure Fitting and Refinement Guided by Cryo-EM Density
Structure 16, 295-307, 2008

iMODFIT 1.51 – Fitting of Atomic Structures into EM maps based on iMOD

iMODFIT 1.51

:: DESCRIPTION

iMODFIT is an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates.

::DEVELOPER

The Structural Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

iMODFIT

:: MORE INFORMATION

Citation

J Struct Biol. 2013 Aug 30. pii: S1047-8477(13)00216-5. doi: 10.1016/j.jsb.2013.08.010.
iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates.
Lopéz-Blanco JR, Chacón P.

Sculptor 2.1.1 – Docking & Visualization for Atomic Structures

Sculptor 2.1.1

:: DESCRIPTION

Sculptor is an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures. We are developing Sculptor as a GUI-based extension of the Situs docking programs, to allow an interactive exploration and analysis of volumetric maps. Sculptor combines 3D rendering with advanced mathematical concepts like clustering techniques and pattern matching algorithms to permit an almost instantaneous fitting of the high-resolution structures and to facilitate typical post-processing work like map editing or resolution adjustment.

::DEVELOPER

biomachina.org

:: SCREENSHOTS

:: REQUIREMENTS

Window / Linux / Mac OsX

:: DOWNLOAD

Sculptor

:: MORE INFORMATION

Citation

Stefan Birmanns, Mirabela Rusu, and Willy Wriggers.
Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes.
J. Struct. Biol., Vol. 173, pp. 428–435, 2011.

MOSBY 0.955 – View Atomic Structures of Protein Molecules

MOSBY 0.955

:: DESCRIPTION

MOSBY ((MOlecular Structure Browser with analYsis)) is a program to view atomic structures of protein molecules. Beyond its basic molecular graphics functions, extension modules provides custom functions for research works in structural biology and computational molecular biology.

::DEVELOPER

Yutaka Ueno, AIST Tsukuba

:: SCREENSHOTS

:: REQUIREMENTS

Linux
C++ compiler

:: DOWNLOAD

MOSBY

:: MORE INFORMATION

Citation

Ueno Y, Asai K.
MOSBY: a molecular structure viewer program with portability and extensibility.
J Mol Graph Model. 2002 Mar;20(5):411-3.