MISTRAL – Multiple Protein Structural Alignment

MISTRAL

:: DESCRIPTION

MISTRAL is a novel strategy for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules.

::DEVELOPER

The Institut de Physique Théorique (IPhT)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Oct 15;25(20):2663-9. doi: 10.1093/bioinformatics/btp506. Epub 2009 Aug 19.
MISTRAL: a tool for energy-based multiple structural alignment of proteins.
Micheletti C1, Orland H.

MultiFit – Fitting of Multiple Proteins into their Assembly Density Map

MultiFit

:: DESCRIPTION

MultiFit is a computational method for simultaneously fitting atomic structures of components into their assembly density map at resolutions as low as 25 Å. The component positions and orientations are optimized with respect to a scoring function that includes the quality-of-fit of components in the map, the protrusion of components from the map envelope, as well as the shape complementarity between pairs of components. The scoring function is optimized by an exact inference optimizer DOMINO that efficiently finds the global minimum in a discrete sampling space.

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W167-70. doi: 10.1093/nar/gkr490.
MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.
Tjioe E1, Lasker K, Webb B, Wolfson HJ, Sali A.

STAMP 4.4.2 – Structural Alignment of Multiple Proteins

STAMP 4.4.2

:: DESCRIPTION

STAMP is a package for the alignment of protein sequences based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit’ superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. If you are after a multiple sequence alignment for proteins of unknown 3D structure, stop reading now and contact GJB for information about AMPS, which can be used to perform multiple sequence alignments, or see www.jalview.org for GJB’s latest methods for this problem.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Window with Cygwin
GCC

:: DOWNLOAD

STAMP

:: MORE INFORMATION

Citation

Proteins. 1992 Oct;14(2):309-23.
Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.
Russell RB1, Barton GJ.