Software
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.
The code is available on GitHub, along with a manual.
Read about the work here:
Staritzbichler R, Yaklich E, et al, 2022 Nucl Acids Res
Staritzbichler R, Sarti E, Yaklich E, et al 2021 PLoS ONE
Stamm M, et al, 2013, PLoS ONE
Khafizov K,et al, 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 on GitHub.
Follow the tutorial described in Lee SP, Bradshaw RT, et al 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, producing confidence scores for each position.
The code is available on GitHub.
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.
Read about the website here: Sarti, Aleksandrova, Ganta, Yavatkar & Forrest, 2019, Nucl Acids Res
A preprint about the underlying database is on the bioRxiv.
2. MemSTATS
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, and the code is available on GitHub.