Lucy Forrest - Prototype 01

Forrest Lab

National Institute of Neurological Disorders & Stroke

Software

1. AlignMe

Align sequences or profiles of membrane proteins, at www.bioinfo.mpg.de/AlignMe where you can:
  • Access the AlignMe Server, hosted by the Max Planck Society Bioinformatics Facility
  • Download standalone version and examples
Version 1.1
  • Position Specific Subsititution Matrices (PSSMs) supported as input
  • Support for ClustalW and fasta format outputs
  • Extract two sequences from the alignment of two averaged MSAs
  • Gaps are now "?0" in profiles - avoids conflation of gaps with zero profile values
  • Scripts for running with optimal parameters for alpha-helical proteins

 Manual for the standalone version of AlignMe 1.1

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


2. Consensus Structure Alignments

Combines several structure alignment outputs and produces confidence scores for each position.

  scripts for computing consensus information from structure alignment programs.

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


3. GRIFFIN

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

Data

1. EncoMPASS

The EncoMPASS (The Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry) database encodes structural relationships between membrane proteins, plus every structure is analyzed for symmetry. The website provides a visual interface for the symmetries and other analysis. The code for generating the database is on GitHub at https://github.com/EncomPASS-code/EncoMPASS
Read about the website here: Sarti, Aleksandrova, Ganta, Yavatkar & Forrest, 2019, Nucleic Acids Res


2. MemSTATS

MemSTATS (Membrane protein Structures And Their Symmetries) is a dataset designed for testing symmetry detection algorithms. The manuscript was accepted for publication in J Mol Biol and is available on bioRxiv https://doi.org/10.1101/653295, the dataset is available on zenodo, and the code is available on GitHub at https://github.com/AntoniyaAleksandrova/MemSTATS_benchmark
DOI



3. HOMEP

A dataset of families of HOmologous MEmbrane Proteins. Membrane proteins of known structure are classified into families with related transmembrane topologies. These can be used as a reference dataset for a range of sequence alignment and structure prediction methodologies specific to membrane proteins. Multiple versions exist and were used for different projects: 

v3 - Used to test membrane protein structure alignment methods
Citation: Stamm M, Forrest LR, 2015, Proteins
DOI

v2 - Used to develop the AlignMe alignment optimal parameters
Citation: Stamm M, Staritzbichler R, Khafizov K, Forrest LR, 2013, PLoS ONE 
DOI

v1 - Original version used to test membrane protein homology modeling methods, when Lucy was in the Honig Lab (http://bhapp.c2b2.columbia.edu/software/Data_sets/homep/)
Citation: Forrest LR et al, 2006, Biophys J
DOI 


 

Lab News

Benchmarking membrane protein symmetry

Congratulations to Dr. Antoniya Aleksandrova for her elegant work creating a benchmark of membrane protein symmetries, just accepted for publication!

Serotonin uptake in gut bacteria?

Recent work with the Hsaio lab shows an intriguing role for serotonin in gut microbe colonization potentially involving transporter-mediated uptake. Congratulations to Dr. Antoniya Aleksandrova & summer student Noah Riley! 

Hitchhiking on lysosomes

Human annexin protein connects lysosomes to RNA granules, with implications for ALS. Congratulations to summer student Matthew and postbac Christina Stephens!

Lucy honored to present the NIH Directors Seminar

Her talk on April 5th titled "Satisfying symmetry: uncovering functional insights from patterns in membrane protein structures" can be viewed here.

 

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