Forrest Lab Resources

Software

 

1. AlignMe

For aligning sequences or profiles of membrane proteins, including a new feature for anchoring individual positions!

Run jobs on the server hosted by the Max Planck Society Bioinformatics Facility at www.bioinfo.mpg.de/AlignMe
The code is available at github.com/Lucy-Forrest-Lab/AlignMe
A manual is available at lucy-forrest-lab.github.io/AlignMe 

Read about the work here:
Staritzbichler R, Sarti E, Yaklich E, Aleksandrova A, Stamm M, Khafizov K, Forrest LR, 2021 PLoS ONE
Stamm M, Staritzbichler R, Khafizov K, Forrest LR, 2013, PLoS ONE
Khafizov K, Staritzbichler R, Stamm M, Forrest LR, 2010, Biochemistry


2. Hydrogen-Deuterium Exchange Ensemble Refinement (HDXer)

To predict hydrogen-deuterium exchange levels for protein structures or simulations, and to re-weight ensembles to reflect experimental target data.

Developed together with the Faraldo-Gómez lab at NHLBI 
The code is available at github.com/TMB-CSB/HDXer
Read about the work here: Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR 2021, Biophysical Journal

 

3. Consensus Structure Alignments

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

The code is available at github.com/Lucy-Forrest-Lab/consensus_struct_align
Read about the work here: Stamm M, Forrest LR, 2015, Proteins
 

4. 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.

Developed together with the Faraldo-Gómez lab at NHLBI. The GRIFFIN pages are currently under construction.
Read the paper: Staritzbichler R, Anslemi C, Forrest LR, Faraldo-Gómez JD, 2011, J Chem Theor Comp

Datasets

 

1. Membrane Protein Symmetry and Structure; 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
A preprint about the underlying database is available here: https://www.biorxiv.org/content/10.1101/391961v1 

 

2. MemSTATS

MemSTATS (Membrane protein Structures And Their Symmetries) is a dataset designed for testing symmetry detection algorithms.

Read about the dataset in the Journal of Molecular Biology 10.1016/j.jmb.2019.09.020
The dataset is available on zenodo: https://doi.org/10.5281/zenodo.3234036
The code is available at github.com/AntoniyaAleksandrova/MemSTATS_benchmark