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SOFTWARE


Align sequences or profiles of (membrane) proteins
available at www.bioinfo.mpg.de/AlignMe where you can: 

- Access the AlignMe Server, hosted by the Max Planck Society Bioinformatics Facility
- Access download of standalone version and examples


Version 1.1 

- Position Specific Subsititution Matrices (PSSMs) supported as an alignment input
- ClustalW and Fasta-Format output of the aligned sequences supported
- extraction of two sequences from the alignment of two averaged MSAs possible
- gaps are now "?0" in the profiles - no more confusion of gaps with profile values having a 0
- added a perl script with the best parameters for alpha-helical proteins to the package
- improved error feedback

  manual for the standalone version of AlignMe 1.1

Cite this: 
Stamm M, Staritzbichler R, Khafizov K, Stamm M, Forrest LR, 2013, PLoS ONE
Khafizov K, Staritzbichler R, Stamm M, Forrest LR, 2010, Biochemistry




Combines multiple structure alignment outputs and produces a confidence score for each position.

  all scripts for computing consensus information from multiple structure alignment programs.

Cite this: 
Stamm M, Forrest LR, 2015, Proteins



Grid-based Force-Field Input: for setting up of membrane protein systems, by treating the protein as an implicit object (on a grid) and expelling the lipids from the region overlapping the protein. Can be run in combination with the standard molecular dynamics packages NAMD or Gromacs.

- GRIFFIN pages may be accessed at faraldolab.org
- Read the paper: Staritzbichler R, Anslemi C, Forrest LR, Faraldo-Gómez JD, 2011, J Chem Theor Comp 7:1167–1176
(doi: 10.1021/ct100576m)