Tag: Electron Density

Ringer – Detect Molecular Motions by automatic Electron Density Sampling

Ringer

:: DESCRIPTION

The program Ringer detects molecular motions by automatic electron density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which part are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design.

::DEVELOPER

Alber Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Ringer

:: MORE INFORMATION

Citation

Lang et al.
Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
Protein Sci.: 2010, 19(7);1420-31.

LSim 1.0.0 – Superposes Macromolecular Electron Densities and Computes Structural Similarity Score

LSim 1.0.0

:: DESCRIPTION

LSim superposes macromolecular electron densities and computes a structural similarity score. LSim computations scale linearly with the size of the molecules being compared.

::DEVELOPER

Pere Constans

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LSim

:: MORE INFORMATION

Citation

Constans, P.
Linear Scaling Approaches to Quantum Macromolecular Similarity: Evaluating the Similarity Function.
J. Comput. Chem. 23, 1305-1313, 2002

buccaneer 1.5 – Electron Density Interpretation/Protein Model Building software

buccaneer 1.5

:: DESCRIPTION

‘buccaneer‘ (BUild Connected C-Alphas, Nautical Excuse for Eponym Required) performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target.

::DEVELOPER

Kevin Cowtan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

.:: DOWNLOAD

  buccaneer

:: MORE INFORMATION

Citation

Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11. Epub 2006 Aug 19.
The Buccaneer software for automated model building. 1. Tracing protein chains.
Cowtan K.

Nautilus 0.2 – Electron Density Interpretation/Nucleotide Model Building software

Nautilus 0.2

:: DESCRIPTION

‘Nautilus‘ (from Greek ναυτίλος, ‘sailor’) is a program for automatic model building of nucleotide structures in electron density maps. It will trace a map with no model, extend an existing model, or add nucleotide chains to an existing non-nucleotide model.

::DEVELOPER

Kevin Cowtan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 Nautilus

:: MORE INFORMATION

CONSCRIPT – Generate Electron Density Isosurfaces in Protein Crystallography

CONSCRIPT

:: DESCRIPTION

CONSCRIPT is a program for generating electron density isosurfaces for presentation in protein crystallography.CONSCRIPT is designed to generate Gouraud shaded isosurfaces of protein electron density for high quality presentation in journals.Electron density maps in protein crystallography are typically presented as “wireframe” or “chickenwire”. Whilst this method has been enormously successful for interactive atomic model building, it is not ideal for presentation. In particular, chickenwire views often appear cluttered and adequate illusion of depth only is achieved with stereo-pair presentation.CONSCRIPT allows protein electron density isosurfaces to be rendered in triangulated form suitable for input into the popular MOLSCRIPT and Raster3d packages. This method of display leads to more easily interpretable pictures and can dispense with the need for stereo-pair presentation.

::DEVELOPER

MC Lawrence & P Bourke

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CONSCRIPT

:: MORE INFORMATION

Citation

MC Lawrence & P Bourke
A program for generating electron density isosurfaces from Fourier syntheses in protein crystallography.
Lawrence, M.C. & Bourke, P. (2000) J. Appl. Cryst., 33, 990-991