Forrest Lab Resources



1. AlignMe

For aligning sequences or profiles of membrane proteins, including new features for anchoring individual positions and visualizing sequence differences mapped onto structures!

Run jobs on the server hosted by the Max Planck Society Bioinformatics Facility at
The code is available at
A manual is available at 

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
Follow the tutorial described in Lee SP, Bradshaw RT, Marinelli F, Kihn KC, Smith AK, Wintrode PL, Deredge DJ, Faraldo-Gómez JD, Forrest LR 2021, LiveCoMS
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
Read about the work here: 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.

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



1. Membrane Protein Symmetry and Structure; EncoMPASS

The EncoMPASS (The Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetrydatabase 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
Read about the website here: Sarti, Aleksandrova, Ganta, Yavatkar & Forrest, 2019, Nucleic Acids Res
A preprint about the underlying database is available here: 



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

Read about the dataset in: Aleksandrova AA, Sarti E, Forrest LR 2020, Journal of Molecular Biology 
The dataset is available on zenodo:
The code is available at